The European Commission is suing the UK at the European Court of Justice (ECJ) for failure to allocate safe marine areas for harbour porpoises.
This month, one site was designated in Scottish waters for protecting the vulnerable species, which lives in various coastal areas around the UK.
The UK government has held a public consultation on five possible sites.
The sites - called Special Areas of Conservation (SACs) - require EU Commission approval before the UK can launch the necessary measures to protect species in them.
"Due to the unfavourable status of the harbour porpoises in the EU, 13 member states, other than the UK, have designated sites for its protection," the Commission said.
"The Commission has repeatedly urged the British authorities to fulfil their key obligations for the conservation of the species, as other member states have done already."
In May, marine biologists told New Scientist that they were worried about a rise in the numbers of porpoises starving to death in UK waters.