The Decarbonization Stack: CII, EEXI, FuelEU and EU ETS in Operational Practice

For most of the last decade, decarbonization in shipping was framed as a strategic horizon — a 2030 problem, then a 2050 problem, always a problem for a successor. That framing is no longer defensible. EEXI is in force. CII has been generating ratings since 2023 and the thresholds tighten each year. FuelEU Maritime entered application on 1 January 2025. EU ETS reaches 100% of in-scope emissions on 1 January 2026. The IMO 2023 GHG Strategy, adopted as resolution MEPC.376(80), commits member states to net-zero by or around 2050.

The implication for commercial operators — ferry, ro-ro, container, dry bulk, tanker, port agency — is straightforward: decarbonization compliance is now an operational system. It runs on every voyage, every bunker delivery, every port call. It generates legal evidence, financial obligations and, increasingly, charter party consequences. This article is a practical view of what that stack must do, and where software is non-negotiable.

Four regulations, one data model

It helps to read the four headline regimes as one data model with four reporting projections.

• EEXI — Energy Efficiency Existing Ship Index. A one-time technical index for ships of 400 GT and above, established under MARPOL Annex VI as amended by MEPC.328(76), in force from 1 January 2023. EEXI is calculated, verified and recorded on the IEE Certificate at the first IAPP renewal survey after entry into force.
• CII — Carbon Intensity Indicator. An annual operational rating from A to E for ships of 5,000 GT and above, established under MEPC.336(76) and MEPC.338(76). The required CII tightens each year on the trajectory toward 2030.
• FuelEU Maritime — Regulation (EU) 2023/1805. A well-to-wake GHG intensity limit on the energy used by ships above 5,000 GT calling at EU/EEA ports, with reduction steps from 2025 through 2050 and pooling, banking and borrowing mechanisms.
• EU ETS — Directive 2003/87/EC as amended by Regulation (EU) 2023/957. Shipping was phased in from 2024 at 40% of reportable emissions, 70% in 2025, and 100% from 2026, requiring surrender of EU Allowances (EUAs) for in-scope voyages.

Each regime asks for a different metric — energy efficiency, carbon intensity, GHG intensity, absolute CO2-equivalent emissions — but the underlying source is the same: voyage-level fuel consumption, distance sailed, cargo or passenger work performed, and the well-to-wake characterisation of every fuel batch bunkered. A fleet that cannot reconcile those four projections from a single ledger will pay for the same data twice and reconcile it three times.

EEXI: technical, but not finished

EEXI is sometimes treated as a closed file because it is a one-time exercise. That underestimates it. The Energy Efficiency Existing Ship Index compares a ship's attained value against a required value derived from its type, size and reference line. Where the attained value exceeds the required, common compliance routes are Engine Power Limitation (EPL) or Shaft Power Limitation (ShaPoL), with override procedures permitted only in defined emergencies and recorded.

The operational consequence is that vessels which complied through power limitation are now sailing with a permanent constraint on their available MCR. That constraint must be visible to charterers, voyage planners and port captains. A speed-distance plan that ignores the EPL is a plan that exposes the operator to non-compliance, charter party disputes, and an underperforming voyage.

CII: an annual rating that is in fact a daily problem

CII is calculated annually and recorded on the SEEMP, but it is decided every sea day. The rating depends on grams of CO2 per deadweight or gross tonnage per nautical mile, integrated across the calendar year. The boundary lines between A, B, C, D and E shift downward each year on the IMO trajectory. A ship rated D for three consecutive years, or E for one year, must submit a corrective action plan in its SEEMP.

From a software standpoint, CII demands four things at minimum:

• Daily fuel and distance data quality good enough to predict the year-end rating, not merely calculate it after the fact.
• A scenario engine that lets a fleet manager test the CII consequence of a slow-steaming order, a re-routing, or a longer ballast leg before issuing instructions.
• Correction factor logic that is auditable: voyages with ice navigation, ship-to-ship transfers, certain port stays and cargo heating may qualify for adjustments under the CII guidelines, but only with documentation.
• SEEMP Part III governance — the corrective action plan is itself a regulatory artefact, not an internal memo.

CII has also re-entered charter parties. BIMCO clauses for time charters require the parties to agree how operational decisions affecting CII are taken and who carries the resulting rating risk. A charterer who orders speeds that depress the rating, and an owner who accepts those orders without documentation, are both exposed.

FuelEU Maritime: where well-to-wake actually matters

FuelEU Maritime is the regulation that finally makes well-to-wake GHG intensity a transactable number for European trades. The annual GHG intensity of the energy used onboard must fall by 2% in 2025, 6% in 2030, and continues on a tightening schedule through 2050, applied to ships of 5,000 GT and above for 100% of energy used on intra-EU voyages and 50% on voyages into or out of the EU.

Three operational features distinguish FuelEU from earlier regimes:

• Well-to-wake accounting. The carbon intensity of a fuel includes its production and supply chain, not only its combustion. A bio-LNG batch with a documented sustainable feedstock is materially different from a fossil LNG batch even when combusted in the same engine. Software must ingest Bunker Delivery Notes plus the sustainability documentation that travels with renewable and low-carbon fuels.
• Banking, borrowing and pooling. A compliance surplus on one ship in one year can be banked for use the next year, borrowed against next year's surplus within strict limits, or pooled across a group of ships. Pooling agreements are commercial instruments. They have to be modelled, not just reported.
• The penalty is real and large. The FuelEU non-compliance penalty applies per tonne of VLSFO-equivalent energy that exceeds the limit and grows for repeated non-compliance. An operator who treats FuelEU as a reporting exercise rather than a planning constraint will discover the financial consequences in the verifier's statement.

EU ETS: shipping is now an emissions trader

The EU Emissions Trading System reached shipping in 2024. The phase-in schedule surrenders EU Allowances for 40% of in-scope CO2-equivalent emissions for 2024, 70% for 2025, and 100% from 2026. From 2026 the scope also expands beyond CO2 to include methane and nitrous oxide for ships above 5,000 GT, and offshore vessels above 5,000 GT come into scope. Smaller general cargo and offshore ships above 400 GT are subject to MRV but not yet ETS.

The practical change is that every commercial shipping company holding an EU MRV Document of Compliance is now an emissions trader, whether it intended to be one or not. That status carries obligations that did not exist in shipping before:

• Open and maintain a Maritime Operator Holding Account in the Union Registry.
• Surrender allowances by 30 September each year for the previous reporting year's in-scope emissions.
• Decide whether to procure allowances spot, forward, through a portfolio manager, or pass-through under a charter clause that allocates the cost to the cargo interest.
• Hedge an exposure that is at once regulatory, commercial and accounting.

EU ETS treatment in charter parties is now a standard negotiation point. BIMCO has issued clauses for both time and voyage charters. The clause itself is a contractual position, but the data that feeds it — voyage-level emissions allocated correctly between owner, time charterer and voyage charterer — is a software output.

The shared backbone: IMO DCS and EU MRV

Underneath the four regimes sit two reporting frameworks that have existed for longer and are now load-bearing.

• IMO DCS — the IMO Data Collection System for fuel oil consumption, established under MARPOL Annex VI Chapter 4, applies to ships of 5,000 GT and above. DCS feeds CII, and the Statement of Compliance from the flag State is a precondition for trading.
• EU MRV — Regulation (EU) 2015/757, monitoring, reporting and verification of CO2 emissions from maritime transport, applies to ships above 5,000 GT calling at EU ports. EU MRV feeds EU ETS surrender obligations and FuelEU GHG intensity calculations.

The two frameworks overlap but are not identical. They use different vessel boundaries, different scope definitions for voyages into and out of the EU, different verifier ecosystems and different reporting calendars. A fleet that maintains parallel spreadsheets for each regime is paying for redundant work and accepting reconciliation risk. The correct architecture is a single voyage data record that projects into DCS, MRV, FuelEU and ETS reports through deterministic logic, with verifier-grade audit trails on every transformation.

What the software must actually do

For sustainability officers and technical superintendents specifying systems, the requirements list is concrete:

• Voyage-level data capture with sufficient quality controls to satisfy a verifier — automatic flow meter readings where available, structured noon reports where not, with anomaly detection and manual override audit logs.
• Bunker fuel ledger that records every BDN, ties each fuel batch to its sustainability documentation, and applies the correct well-to-wake emission factor to each consumption event.
• Multi-regime calculation engine that produces EEXI cross-checks, CII per voyage and year-to-date, FuelEU GHG intensity per ship and per pool, and EU ETS allowance liability per voyage with the in/out-EU scope rules applied correctly.
• Forecast and scenario tools that run before voyage instructions are issued, not after. CII rating and FuelEU compliance both reward early adjustment and punish late discovery.
• Verifier-ready reporting for IMO DCS, EU MRV, FuelEU verifier statements, and ETS surrender, in the formats that flag administrations and accredited verifiers actually accept.
• Allowance and pooling management — Union Registry accounts, EUA holdings, surrender schedules, and FuelEU pooling agreements modelled as the financial instruments they are.
• Charter party data flows so that time charterers, voyage charterers and owners can see, in near-real-time, the CII, FuelEU and ETS implications of operational decisions.

What fleets cannot defer

If a fleet is reading this in 2026 and is still treating decarbonization compliance as a project, the priority order is clear. Establish a single voyage and bunker ledger this year. Operationalise CII forecasting before the next year-end. Bring FuelEU pooling decisions into commercial planning rather than year-end reporting. Open and fund the Union Registry account before 30 September deadlines force last-minute allowance procurement at unfavourable prices. Align charter party clauses to the data model the company actually has, not the one it wishes it had.

Decarbonization regulation will keep tightening. EEXI will be revisited. CII thresholds drop. FuelEU steps grow. EU ETS expands beyond CO2 and beyond European waters as analogous regimes emerge in the United Kingdom and elsewhere. The IMO mid-term measures, expected to enter into force later this decade, will likely add a global GHG fuel standard and a global pricing mechanism that will sit alongside, and partially overlap with, the EU framework rather than replace it. The fleets that handle the next ten years well will not be the ones that buy the most software. They will be the ones that build a clean voyage data record, govern it as a regulated asset, and treat every new regulation as another projection of it.

SupaMaritime works with commercial operators on the operational backbone behind these regimes — bunker accounting, voyage and emissions data, charter party flows, port and agency workflows. Explore the modules built for fleets and ferry operators on merchant fleet operations and ferry operations, see the platform overview on modules, and review our approach to data integrity on security.