A "flag-link" proposal from the European Union could affect tonnage tax schemes already in operation in many EU member states. State aid for shipping is already permitted by the EU but the latest communication from the European Commission on guidelines for maritime transport subsidies stresses the need for a link with the flag.

So called "flag-neutral" tonnage tax schemes, such as that operated by the UK, will be allowed to continue, but Brussels wants shipping companies operating less than 60% of their tonnage under an EU flag to have at least the same tonnage EU-flagged when the communication enters into force.