You are probably looking to transport products between Malaysia and Indonesia. You are in the right place! We will give you some valuable information on this topic to help you see more clearly about means of transport, regulations, customs procedures, etc.. DocShipper Malaysia, from the DocShipper group, has sorted all this information for you.

DocShipper info: FNM Malaysia is an international freight forwarder that handles all of your needs by operating as your single point of contact with all the logistics service providers. Relax because we take care of everything, packaging, organizing transport, customs clearance, administrative procedures, and regardless of the shipping method (air, sea, road, rail). Contact us or call us to receive a free quote in less than 24 hours.


Table of Contents

The different methods of transportation between Malaysia and Indonesia

To connect Malaysia and Indonesia, the two types of means of transport are: Sea freight and air freight

We have listed two major ways below and compare each of them, from advantages to disadvantages, from ports to airports. Comparisons are made, and you only need to choose what suits you best.

Sea freight between Malaysia and Indonesia

Overview - Ocean freight between Malaysia and Indonesia

The two countries are connected by a maritime corridor in Southeast Asia, which is the famous Strait of Malacca.
This long sea corridor is located between the Malaysian peninsula and the Indonesian island, extending over 930 km, with a width between 50 and 390 km.
The proximity of the two countries makes it possible to carry out commercial transport with a fast ride.

The Strait of Malacca is an important and strategic crossing point in southeastern Asia, with more than two-thirds of the oil and gas flows through it.
The shipping route taken by oil tankers through the Strait of Malacca is the shortest and fastest between the Persian Gulf and East Asia, which is also very economical.

The busiest strait in the world is Malacca, with over 100,000 merchant ships passing through it.

The main shipping seaports in Malaysia

Port of Kelang

The port of Kelang is located on the Strait of Malacca. With its 573 km² area, it ranks 16th world port and 1st of Malaysia. Formerly a transshipment port, the port has been able to take advantage of the saturation of the port of Singapore to accommodate many container ships. CMA-CGM has made it its main hub in Asia.

Port of Tanjung Pelepas

The port of Tanjung Pelepas is located at the mouth of the Pulai River. It is the largest container terminal in Malaysia. Since its construction in 2000, it has evolved and managed to rank 17th in the world for containers. The port offers reliable, efficient and advanced services to major shipping companies and box operators, offering shippers in Malaysia and abroad extensive connectivity to the global market. The Port of Tanjung Pelepas is a joint venture between MMC Corporation (70%), a utility and infrastructure group and APM Terminals (30%), a leading global port group with a global network of ports in 69 countries.

The main shipping seaports in Indonesia

Port of Bakauheni

Bakauheni is a town in the south of Lampung province, Indonesia. This port has a great influence in the city, because the flow of ferries is done in large numbers. On average, every 12 minutes, a ferry leaves the port. The port of Bakauheni is one of the busiest in Indonesia.

Port of Tanjung Priok

Tanjung Priok port is the busiest seaport in the country and the most advanced. The port is located in Tanjung Priok, North Jakarta, which is held by the Indonesian state PT Pelindo port loaded and unloaded 6.2 million, 6.92 million and 7.8 million TEUs of cargo in 2016, 2017 and 2018 respectively, out of a total capacity of about 8 million TEUs. The container port ranked as the 22nd busiest in the world by Lloyd's Cent Ports.

Port of Surabaya

Tanjung Perak Port is the second busiest seaport in the country, located in Surabaya, East Java. It is the main port for the eastern part of the island of Java. The port is accessible from the north through the Madura Strait, a 40 kilometer long, 110 meter wide and 31 feet deep channel between East Java and Madura Island. Due to its advantageous position, the seaport is the inter-island shipping center for eastern Indonesia. The container terminal of the port is known as Petikemas Terminal. The port loaded and unloaded 3.55 million and 3.8 million TEUs of cargo in 2017 and 2018 respectively. In 2020, Tanjung Perak ranked as the 45th largest port in the world.

Transit time between Malaysia and Indonesia ports

Transit time between Malaysia and Indonesia ports

Indonesia / Malaysia   Port of Kelang   Port of Tanjung Pelepas
Port of Bakauheni   4-7 days   1-5 days
Port of Jakarta   4-7 days   4-6 days
Port of Surabaya   5-6 days   1-5 days


DocShipper Alert : We are experts in freight forwarding. Do you need to ship your goods from Malaysia to Indonesia by sea? We are here and are able to take care of everything for you to help you save time and money! Contact us via our form or by phone for more information about sea freight and a free quote.


Please note that transit times are an average of days onboard the vessel and do not include pre-carriage, delivery, and customs clearance. Besides, sea freight being the slowest method, you need to schedule departure

Do I have to ship by groupage or full container between Malaysia and Indonesia?

There are several types of containers, but 3 sizes are the most commonly used :

  • 20 feet (33 cubic meters capacity)
  • 40 feet (67 cubic meters capacity)
  • 40 feet HQ (High Cube, 76 cubic meters capacity)

Let's take a look at the two methods of transportation :

Less than Container Load (LCL)

When your cargo does not fill an entire container, LCL shipping is a good option. In addition, it allows you to simply pay for the amount of space you really need, making it ideal for smaller deliveries. Your merchandise will be placed next to that of another merchant moving in the same direction.

Full Container Load (FCL)

This means that between the time of departure and the time of arrival, only one consumer uses the entire container. The container will be sealed as soon as it leaves the company’s property until it is delivered to the customer to minimize risk and expense.

It is a good means of transportation to use if you intend to buy a lot of products.

Therefore, no matter if you complete it completely, FCL will be safer and cheaper for more. Unquestionably, from 15 m³, a full container can be cheaper than LCL.

Special maritime transport between Malaysia and Indonesia

There are a number of factors that determine the type of container you will need, including the size of your shipment, as well as the commodity. If you are about to ship specific goods, the below are available.

Reefer container

The refrigerated container is a thermally insulated container with a temperature maintenance device. It allows the transport of goods under controlled temperatures. It is often used for foodstuffs or chemicals.


A Ro-Ro is a vessel used to transport, among other things, vehicles, loaded by one or more ramps. They are also called Ro-Ro, from the English roll-on/roll-off meaning literally "roll, roll, roll", to distinguish them from the usual cargo ships where products are loaded vertically by cranes


Bulk goods are products transported directly into the ship's hold or into the facilities provided for that purpose. A distinction is made in this case between bulk goods and general cargo. Solid bulk goods : (such as coal, ferrous and non-ferrous ores) liquids in bulk: (petroleum and petroleum products). Bulk goods are transported by bulk carriers, specialized vessels for each type of cargo: ore carriers, coal carriers, etc.).


OOG (Out of Gauge) cargoes are a special category of goods. Because of, for example, their non-standard dimensions or weight, some goods cannot be loaded in traditional containers. These types of cargo are usually loaded on a platform or trailer for transport.

Do not hesitate to contact our experts for any request concerning special transports. Our services are empowered to advise you and offer you the best solutions. Do not hesitate to consult our web page which deals with sea freight.

How much does sea freight between Malaysia and Indonesia cost?

When you decide to export or import, it is very important to know the weight but also the volume of your goods. Indeed, transport pricing is always based on the weight/volume ratio.

You have two options :

  • In groupage (goods in bags, crates, drums, etc...). This chargeable unit can be the tonne or the m³ to the advantage of the carrier, according to the weight/volume equivalence rule 1t = 1m³. The higher of the two will be taken to the advantage of the carrier.
  • In full containers, the freight is calculated on a flat rate per container, which takes into account the type of container but is independent of the type of goods carried.

For all requests, do not hesitate to contact our sea freight expert by filling out our online form.

Tariff supplementation

Maritime tariff surcharges are charges levied by maritime transport providers in addition to the negotiated party-agreement tariff and which depend on a specific context.

The pricing of freight transport by sea is characterized by its complexity

BAF : Bunker Adjustment Factor

This tariff surcharge corresponds to fluctuations in the price of crude oil. Given the consumption of modern ships, shipping companies began to apply it after the first oil crisis in 1973. It has remained on the agenda ever since

CAF : Currency Adjustment Factor

This surcharge corresponds to fluctuations in the value of the dollar. As the vast majority of ocean freight rates are calculated in US dollars, companies hedge against currency risks with this surcharge

THC : Terminal Handling Charge

THC represents the handling charges at the port of loading and unloading. The amount may be fixed in the case of a container (price per container) or variable in the case of conventional (i.e. "non-containerised") cargo. In the latter case, the rate is per tonne and may be subject to various surcharges (for "excessive" size or weight).

Air freight between Malaysia and Indonesia

Classic or Express air freight

Air shipments are also a common mode of transportation for many importers across Asia. Air cargo is a safe, fast and efficient means of transportation between these two territories.

The two methods are quite different from each other, both in terms of price and service :

Conventional air cargo will exploit the space available on conventional airlines such as Malaysia Airlines, Air Asia

Express air freight will use the network of courier companies such as DHL, FedEx, TNT, UPS...


logo courrier company

two distinct forms of transportation

What are the advantages of air transport?

The best thing about air travel is speed.

In general, the transit time between Malaysia and Indonesia does not exceed 7 working days. In most cases, it’s only three to five days. That’s a significant reduction compared to marine cargo. Today, fast delivery times can have a huge impact on a niche market.

Please note that air cargo is only one link in the supply chain. Indeed, in addition to air cargo, you will also need (at a minimum) export and import services, including airport fees, customs declaration, etc. This is of course a service that DocShipper offers.

How much does air freight transport between Malaysia and Indonesia cost?

When shipping by air cargo in the future, it is important to consider all the costs you will have to face when shipping. We are thinking in particular of airport charges, documentation and reporting fees, customs duties and taxes...

For air cargo, it will be charged by weight, by Kgs. Please note that conventional air cargo is still much cheaper by Kgs than express cargo. Finally, the carrier, whether an airline or a postal agency, will consider the most important value between gross weight (on the scale) and dimensional weight (depending on dimensions).

How do you calculate the volumetric weight of your shipment?

For conventional freight, the basic rate is a weight band rate, rapidly decreasing, with a minimum charge for very small shipments. On the same principle, express freight also offers a rate per step depending on the volume you are shipping. As indicated just above, the carrier will base the rate on the greater of the gross weight and the volumetric weight, which is calculated as follows:

  • Conventional Air Freight: 1 m³ = 167 Kgs
  • Express Air Freight: 1 m³ = 200 kgs 

Docshipper Tip : As a freight forwarder, we are also providing air freight services to handle your shipment when you are in a rush and need the operation to be completed quickly. Don't hesitate to contact us or call us for more information about air freight and a free quote!



Docshipper Tip: Because we want to provide the most valuable and comfortable service to our customers, we propose door-to-door shipping, so you don't have to worry about your shipment from the beginning to its arrival in the recipient's office. Contact us or call us for more information and a free quote!


DocShipper recommendations

The airway will be the fastest method you have at your disposal, but it may also be the cheapest! Do not hesitate to contact our team for more information on what solutions are available to you and at what price. Fill out our online form for quick feedback from our experts.

We also put at your disposal our internet page which talks about air cargo.

Custom Clearance in Malaysia

In Malaysia, in order to perform customs clearance of your goods, a full invoice and air waybill are required. If the item being shipped is controlled/restricted or prohibited, an additional permit or licence may be required by the authority

In Malaysia, your goods will only be cleared and accessible once all duties and taxes have been paid. A shipment may be cleared prior to arrival. Otherwise, if there are problems with your merchandise and/or documentation, the release of the shipment may take 24 to 48 hours after the arrival of your goods.

Custom Clearance in Indonesia

Like in Malaysia, In order to clear your goods, you must bring your full set of complete invoice and the air waybill. If your goods contain dangerous, restricted or prohibited goods, the customs service will ask you to declare them in advance.

What are the customs duties and taxes?

The Harmonized Commodity Description System (HS) is used in Malaysia and Indonesia. As elsewhere, imported items are subject to customs duties. In addition to tariff restrictions, your items may also be subject to VAT and other taxes, which we discuss in more detail below. Goods imported into Vietnam are subject to VAT, Special Consumption Tax (SCT) and possibly Environmental Protection Tax (EPT), in addition to customs taxes (EPT). The type of goods determines the tax rate. For example, taxes on luxury goods are often higher than those on industrial tools or raw materials.

  • VAT rates in Vietnam are either zero, 5% or 10%.
  • STC rates start at 7% and can go up to over 100% for some products such as cars. Cigarettes and other tobacco products, for example, have been taxed at 75% since January 2019.

We have prepared a web page that explains the customs clearance process.

How to get your HS code?

The safest and most efficient way is to ask your seller.

If he is not able to provide it, go to this site: HS code

Utilizing it is pretty simple. Enter your term into the search field and view the results that appear. Take "pineapple" once more as an example.

How to get HS code

Calculating customs duties with the HS code

Do you know what your HS code is? It's time to verify how many taxes will need to be paid on your shipment now. Simple steps are as follows:

Visit the webpage for Vietnamese customs first: Tariff for Malaysians Customs

You must first enter your information (in this example, the HS code and the country of origin, which is Malaysia) : 

vietnam customs webpage

Are you done?  All that's left to do is click the search button to reach the following page :

HS code vietnam customs webpage

How to calculate customs duties and taxes

  • To find the value of the customs duty, you need to add the total value of the imported product to the consumption tax (if applicable) + environmental protection rate (if applicable) x tax rate. 
  • To calculate the VAT, the total value of the imported product + import tax) x VAT rate
  • To calculate the special consumption tax, you simply multiply the value of the product by the applicable SCT rate. 
  • To calculate the environmental protection tax, you simply multiply the quantity of taxable goods by the EPR rate 
  • Finally, if you wish to calculate all the taxes applicable to importing into Vietnam, simply do the following calculation:  import tax + VAT + TCS (if applicable) + EPT (if applicable

Does Docshipper charge duty?

As part of your normal obligations, we will not take payment. In order to demonstrate this to you, we will return the data that has been provided by Vietnamese Customs. Only the expenses related to the creation of a regulatory information document will be subject to an indulgence. Since we will be creating the necessary documents for you, DocShipper will be responsible for collecting these customs leniency fees. The government will be responsible for collecting the customs-related fees.

Docshipper Tip: If you have any questions about international logistics, do not hesitate to ask our experts, they'll be happy to answer your questions! Contact us to get a free quote by filling out our form or calling us!


DocShipper Advice : More than 10 years of expertise on the Asian continent, allows us to offer tailor-made freight solutions at more than competitive prices. Do not hesitate to contact our dedicated specialists for more information on your transfer, we are always happy to serve and disseminate our knowledge, we respond within 24 hours! Contact us by filling out our form or call us to get a free quote in 24 hours.


Our additional services

DocShipper Advise : We help you with the entire sourcing process so don't hesitate to contact us if you have any questions!

  • Having trouble finding the appropriate product? Enjoy our sourcing services, we directly find the right suppliers for you!
  • You don't trust your supplier? Ask our experts to do quality control to guarantee the condition of your goods!
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  • You don't want to handle distribution? Our 3PL department will handle the storage, order fulfillment, and last-mile delivery!


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