EU Emissions Surcharge Audit: How to Check Published Carrier Rates

An EU emissions surcharge on your freight invoice doesn't necessarily mean the amount is correct. The first check is simple: compare what you were billed with what the carrier published for that shipment, on the date its own terms say applies.

Since 2024, most container shipments to or from Europe have carried an extra line on the invoice, tied to the EU Emissions Trading System (EU ETS). Carriers call it different things, such as "Emissions Surcharge", "ETS Surcharge" or "Emission Allowance Surcharge", publish it in their own tariffs, and revise it every few months. For Latin American importers and exporters trading with Europe, it is now a recurring cost that changes more often than most surcharges, which makes it easy to bill wrong.

This article covers one narrow, practical check: whether the emissions surcharge on your invoice matches the surcharge the carrier published for your shipment. It does not judge whether the surcharge is fair, or whether it reflects the carrier's real carbon costs. It asks whether you were billed what the carrier's own published terms say.

100%

Of 2026 emissions covered by allowances, after 40% for 2024 and 70% for 2025

50%

Of emissions covered on voyages between an EU and a non-EU port

3 gases

CO₂, with methane and nitrous oxide added from 2026

30 Sep

Yearly deadline for shipping companies to surrender allowances

What the EU ETS requires of shipping

The EU ETS is a cap-and-trade system. Covered companies must surrender one EU Allowance (EUA) for each tonne of greenhouse gas, measured in CO₂-equivalent, that they emit within scope. Under Directive (EU) 2023/959, maritime transport has been in the system since 1 January 2024.^1,2

• Who carries the obligation. The shipping company: generally the shipowner, or the company that has taken over responsibility for operating the ship. Not the cargo owner. The Directive lets the shipping company recover the cost from whoever buys the fuel or operates the ship, but it sets no surcharge for shippers.
• Which ships. Cargo and passenger ships of 5,000 gross tonnage and above. Offshore ships of that size join from 2027. Smaller general cargo and offshore ships (400 to 5,000 GT) have reported emissions since 2025, and their inclusion in the ETS is under review.
• Which voyages. 100% of emissions on voyages between two EU/EEA ports and while at berth in EU/EEA ports. 50% of emissions on voyages that start or end outside the EU/EEA, which is the share that usually applies to Latin America–Europe trade. A call at a designated neighbouring container transhipment port, currently Tanger Med and East Port Said, does not break the voyage.
• Phase-in. Allowances for 40% of 2024 emissions, 70% of 2025 emissions, and 100% from the 2026 emissions year, surrendered by 30 September of the following year.
• More gases from 2026. Methane (CH₄) and nitrous oxide (N₂O) count toward the obligation alongside CO₂. Both were already monitored from 2024. Methane matters most for LNG-fuelled ships, where unburned fuel can escape.

2026 combined full coverage with the added gases, and carriers revised their surcharges to match. Hapag-Lloyd, for example, told customers in late 2025 that it expected its ETS surcharge to rise substantially for 2026.^6,7 A rate change at a year or quarter boundary is exactly where invoices most often pick up the wrong tariff version.

The legal obligation is not the surcharge

EU law does not fix the surcharge amount. A published-surcharge audit therefore checks the invoice against the carrier's published terms and your contract, not against the regulation.

What this audit checks, and what it doesn't

In scope: the carrier's published surcharge amount for your trade lane and service; the container or equipment type, where the tariff distinguishes (20' or 40' dry, high cube, reefer); the charging unit (per TEU, per container, per shipment, or per weight or volume for LCL); the tariff's effective date; the shipment or contractual event date the carrier's terms use to select the rate; and the amount actually invoiced.

Out of scope: recalculating the vessel's actual emissions, checking what the carrier paid for its allowances, judging its margin on the surcharge, certifying emissions reports, or deciding whether a surcharge is fair, reasonable, lawful or unlawful. Those questions belong to the shipping company, its accredited verifier and the authorities under the EU's monitoring, reporting and verification (MRV) rules.³ A published-surcharge audit is ordinary freight invoice auditing: comparing a billed charge with the rate that should have applied.

Where billing discrepancies come from

• Outdated tariff. Carriers revise ETS surcharges on a regular cycle, often quarterly. An invoice built from a superseded rate table bills the old amount.
• Wrong date basis. Each carrier's terms say which date selects the rate. Maersk, for example, uses a "Price Calculation Date": for most contract bookings, the scheduled departure of the first sea leg at booking confirmation; for U.S. FMC-regulated cargo, the last container gate-in.⁴ An invoice priced on the invoice date, actual sailing or arrival can put a shipment near a rate change into the wrong period.
• Wrong equipment classification. Reefer rates are usually higher than dry, and 40' rates differ from 20'. A dry box billed at the reefer rate is an error.
• Wrong unit or quantity. Per-TEU and per-container rates confused, a container count that doesn't match the bill of lading, or a per-shipment charge applied more than once. A rate can be right in isolation and the total still wrong.
• Wrong lane or service. Rates vary by trade and sometimes by direction. One trade's rate should not be assumed to apply to another.
• Contract terms ignored. Some contracts include, cap or fix the emissions surcharge differently from the public tariff. Then the contract is the benchmark.
• Currency and duplication. A tariff in EUR billed in USD at an undocumented exchange rate, or the same surcharge on both the freight invoice and a local-charges invoice.
• Scope. A charge on a shipment the carrier's own terms exclude, for example with no EU/EEA port in the ocean routing. Separate schemes, such as the UK ETS that Maersk applies from 1 July 2026, should appear as their own lines under their own terms.⁵

How to check an invoice, step by step

1. Pull the carrier's published notice. Use the carrier's own notice or tariff, not a third-party summary. Record the surcharge name, amount, currency, trade lane or service, equipment type, charging unit, effective date, and any conditions. Save every version around your shipment dates, not just the current one.
2. Check your contract first. If your service contract or quote covers the emissions surcharge, that is the benchmark. The public tariff applies where the contract points to it or is silent.
3. Establish the applicable date. From the booking confirmation and bill of lading, collect the booking date, gate-in, scheduled and actual departure. Then apply the date the carrier's terms specify. Never assume the invoice date decides.
4. Match the shipment to the tariff. Run it field by field, as in the table below.
5. Recalculate the expected charge. Published rate × correct quantity, in the tariff currency, with any documented exchange rate.
6. Classify and document the result. Matches, discrepancy, or requires clarification when the documents are incomplete or conflict. A difference is a finding to raise with the carrier, not proof of an overcharge.

A worked example

All figures below are hypothetical, for illustration only. They are not any carrier's tariff or an actual audit finding. A carrier publishes two consecutive surcharge periods and prices on the scheduled first-leg departure at booking confirmation. A shipment's sailing slips across the boundary.

The invoice appears to have used the actual departure date, and so the period B rate. The carrier's stated date basis points to period A, so the line is worth querying. Whether the EUR 80 is recoverable depends on the contract, the carrier's full terms and the carrier's response.

What to collect before you dispute

• The invoice and any credit notes already issued.
• Booking confirmation and bill of lading: scheduled departure, booking date, ports, equipment types and counts.
• Your service contract, rate agreement or quote.
• The carrier's published notices for every relevant period, saved with the date you downloaded them.
• Gate-in records and the vessel schedule, where the date basis depends on them.
• A finding record: shipment reference, invoice number, notice used, applicable and shipment dates, published and invoiced amounts, difference, exchange-rate basis and the reason for flagging.

Checklist for freight finance teams

How Trazai helps

Trazai is a freight audit and intelligence company serving businesses across Latin America. A published-surcharge check is one application of what we already do: freight invoice auditing. We compare billed charges against the applicable contracts and published or regulated tariffs, flag the discrepancies, and prepare documented findings you can take to the carrier. Trazai Pulse, our freight intelligence platform, monitors tariff and rate changes so the reference rates are on file when invoices arrive.

To be clear about the limits: we do not verify emissions or certify EU ETS compliance, and whether a given surcharge can be checked depends on having the carrier's published notice for the relevant period and your shipment documents.

The EU ETS surcharge may reflect a real regulatory cost, but that doesn't remove the need to check what you were billed. As the schedules keep moving, a clear comparison between the applicable published rate and the invoiced amount is the foundation of a defensible surcharge audit. To learn more, visit trazai.lat or request a freight audit below.