Port references and S-numbers: What exporters need to know for container loading at seaports

Key points at a glance

• Every container loaded via a seaport terminal requires a port reference as customs release. Without it, loading cannot take place.
• The reference designation depends on the port. In Hamburg, Z, B and S numbers apply through the ZAPP/EMP system. In Bremen and Bremerhaven, the BHT reference applies. In Wilhelmshaven, the WHT reference applies.
• If the reference is missing or submitted too late, the container remains at the terminal and may incur storage fees and demurrage. This can often be avoided by requesting the reference in good time before delivery and the loading deadline.

What are port references at seaports?

Port references, also known as harbour references in Germany, create the electronic link between customs clearance and terminal processing in the export process. Through the relevant port telematics system, freight forwarders and shippers submit export data to customs and the terminal, check the shipment status and receive the release number required for loading.

In Hamburg, this task is handled by the ZAPP/EMP system. ZAPP stands for Customs Export Monitoring in the Paperless Port. It is connected to the German customs system ATLAS-AES and enables automated electronic export processing.

The basic principle applies across German seaports. Only after customs has granted permission to exit and the port reference number is available may the container be loaded onto the vessel.

Which reference number applies at which port?

Each German seaport uses its own telematics system and therefore its own reference system. The following overview lists the common references.

In Hamburg, the distinction is based on the customs status of the goods. The Z-number is the standard for Union goods with an Export Accompanying Document, the S-number applies to non-Union goods, and the B-number covers special cases. In Bremerhaven and Wilhelmshaven, references are assigned sequentially without this distinction.

If shipments also pass through international ports, similar logic applies with different systems. In Rotterdam and Antwerp, for example, port declarations are handled through Portbase. The principle is the same: no loading without a valid declaration.

How is a port reference generated?

The typical process can be explained using Hamburg’s ZAPP/EMP process. Bremerhaven and Wilhelmshaven follow a similar pattern.

1. Port order: When the goods are presented, the freight forwarder sends a port order to the system and to the terminal. This order already contains the necessary information, such as the vessel and terminal used for the export.
2. Gate-in: The terminal reports the arrival of the container at gate-in. This notification triggers automated submission to the ATLAS customs system.
3. Customs release: Once ATLAS grants permission to exit, the port system generates the reference number and sends it to the parties involved.
4. Loading: Only after the reference is available can the container be loaded onto the vessel at the terminal.
5. Loading notification: Once loading is complete, the terminal reports completion back to the port system. ATLAS is then automatically sent the export confirmation.

The sequence matters. Customs release must be available before the container is loaded. If it is not available at the scheduled time, the chain comes to a stop.

What documents are needed for customs clearance?

The documents required for the port reference depend on the customs status of the goods.

• For Union goods, meaning EU goods, you usually need the Export Accompanying Document and the shipping line’s booking confirmation. The Export Accompanying Document is generated as part of the electronic export declaration via ATLAS and includes the MRN, the Movement Reference Number. It is generally required for exports with a value of EUR 1,000 or more, or a weight exceeding 1,000 kilograms.
• For non-Union goods, meaning non-EU goods, you usually need the T1 transit document, the ATB number and the booking confirmation. The ATB number is the reference for temporary storage. It is assigned when the summary declaration is submitted, and customs uses it to monitor the goods until they are placed under a customs procedure. Temporary storage is time-limited, generally 90 days under Article 149 of the Union Customs Code.

Complete and timely submission of documents is essential for the reference to be generated without follow-up queries.

What happens if the port reference is missing, incorrect or submitted too late?

The most common error is easy to describe: the container is delivered to the terminal without a port reference. The consequence is just as clear. Without a valid reference, the container will not be loaded. It remains at the terminal and may miss the booked vessel.

Two types of additional costs can arise from the longer dwell time: terminal storage fees and shipping line demurrage. At Hamburg, for example, HHLA terminals charge surcharges of EUR 50 per TEU per day for extended dwell times and, in cases of very long dwell times, flat fees of several hundred euros per container. These specific rates apply to imports, but they illustrate the cost logic that can also affect export containers left behind. The exact amount depends on the terminal, the shipping line and the individual case.

In addition to missing references, incorrect or delayed information can lead to the same result. The container cannot be cleared, and dwell time continues to accumulate.

How can delays and additional costs be avoided?

The most effective measure is to place the order in good time. The port reference should be available before the container is delivered to the terminal, not after. This leads to several practical recommendations.

• Request the reference before delivery and before the loading deadline: Allow enough processing time. In Bremerhaven, BHT clearance with the Export Accompanying Document and MRN already available can often take place within a few hours, but otherwise may be delayed. For Wilhelmshaven, the WHT reference must be available before delivery in any case.
• Check slot booking requirements: In Hamburg, slot booking is mandatory for truck deliveries. Containers are only accepted during the booked time slot. This also requires prior clearance.
• Do not deliver too early: Terminals may reject export containers that are delivered too far in advance of the vessel’s arrival. Follow the designated delivery window.
• Submit all required documents: Check in advance whether the required documents are available, depending on the customs status of the goods. For Union goods, this normally means the Export Accompanying Document and booking confirmation. For non-Union goods, this normally means the T1, ATB number and booking confirmation.

And what about imports?

Even though the port reference is primarily an export issue, similar logic applies to imports. A container left at the terminal after unloading cannot be picked up until its customs status has been clarified, for example through presentation to customs and transfer from temporary storage to a customs procedure.

If clearance or pickup is delayed, storage fees and demurrage may also apply. The principle is the same in both directions: first customs clearance, then movement of the container.

How Gerlach supports you

Gerlach Hamburg handles export clearance and the procurement of port references for seaport shipments, regardless of the carrier and with local expertise at the relevant locations. We prepare the necessary customs documents, declare shipments on time and monitor their status so containers can be loaded as scheduled and avoidable demurrage costs are prevented from the start.

This helps companies keep seaport exports moving while the customs side runs reliably in the background.