Britain is facing a referral to the European Court of Justice within two months unless it designates more protection sites for harbour porpoises, a threatened species in the North Sea.

Harbour porpoises are the most common, and smallest, cetacean species found in UK waters. Similar in appearance to bottlenose dolphins, they are very social animals, rotund in shape with a small dorsal fin that shows above the waves.

Although they are still relatively abundant, their numbers are thought to be falling fast under pressure from human activities such as fisheries bycatch, starvation, underwater noise and injuries from boats.

According to the European commission, which sent the UK a warning letter on Thursday, a failure to apply the Habitats Directive to the cetaceans now could “seriously compromise their ecological character”.

“Despite a large number of harbour porpoise in its waters, the UK has so far proposed only one small site in Northern Ireland [as a protected area], exposing some of the identified sites to the risk of offshore wind farm development,” a statement says. “The commission has repeatedly urged the UK to fulfil its key obligations for this species, but no further designations of sites have been proposed.”

Conservationists say that important porpoise habitats should be protected in Scottish waters such as the Hebrides and outer Moray Firth, and in Welsh waters around northern Pembrokeshire and southern Cardigan Bay, in Lleyn Peninsula, Bardsey Island and north and west Anglesey.

In English waters too, critical porpoise habitats could be extended across migration routes, such as the Dogger Bank in the North Sea - where the animals already receive protection in German and Dutch waters.

“Where high densities of porpoises and other mobile species can be found, marine protected areas (MPAs) are required,” said Sarah Dolman, a programme manager for Whale and Dolphin Conservation. “MPAs can help to provide certainty to marine users, enable implementation of local management measures, as well as promoting conservation research and education, and so can aid protection of an often forgotten, coastal species.”

In a flurry of other infringement case announcements, the UK was given two months to reduce nitrogen oxide emissions from the Aberthaw power plant in Wales, while Portugal was given a court referral for inadequate waste water treatment, with a request for a €4.5m (£3.5m) lump sum fine and daily €20,000 penalty until the country complies with EU laws.

The outgoing commission also sent formal notice of a court case over continued finch-trapping by Malta, the home of the EU’s new environment commissioner Karmenu Vella.

That case will be closely watched, as the new EU president-elect, Jean-Claude Juncker, has instructed Vella to conduct “an in-depth evaluation of the Birds and Habitats directives” with a view to merging them in a new law that is “fit for purpose”. Environmentalists consider this a euphemism for deregulation.

The spate of new infringement notices were launched as the EU concluded a public consultation on “biodiversity offsetting”, or a proposed market mechanism that would create new natural sites to compensate for destroyed forests, woodlands, and wildlife habitats elsewhere.

A petition signed by 9,500 people and 60 organisations was handed in to the commission denouncing the proposal as a “license to trash”.

In the UK, the scheme has already allowed plans for supermarkets, service stations and housing developments to proceed, despite community objections to the destructive effects on their local environment.

Opponents say that by giving development plans green credentials that may be spurious, offsetting speeds up planning approvals in practice, and limits natural environments for flora and fauna in absolute terms.

“Biodiversity offsetting commodifies nature and sends out a dangerous message that nature is replaceable,” the petition says. “Biodiversity and ecosystems are complex and unique. It is impossible to reduce biodiversity into a system of credits as envisaged by many offsetting systems. Biodiversity offsetting masks the fact that when you destroy nature, it is lost forever.”

A spokesperson for Defra said: “We are committed to protecting the harbour porpoise. The species benefits from a protected area at Skerries and Causeway, and we are working to identify further potential sites for increased protection.

“We are considering the Reasoned Opinion from the European Commission and will respond in due course.”