The Regulation applies differently to voyages as follows:

Intra-EU Voyages: Entire (100%) energy used on voyages between ports under the jurisdiction of Member States.
Voyages to or from Outermost Regions: For voyages that start or end in an outermost region under the jurisdiction of a Member State, the Regulation applies to ships for one half (50%) of the energy used.
International Voyages: For voyages between a port under the jurisdiction of a Member State and a port under the jurisdiction of a third country (or vice versa), the Regulation applies to ships for one half (50%) of the energy used.