In their complaint, the organisations including the Environmental Justice Foundation and ClientEarth accused the three countries of "seriously and systemically failing to protect vulnerable marine ecosystems in violation of EU law".

Deep-sea bottom trawling -- where a weighted net is dragged along the seabed, which critics say seriously damages ecosystems in the process -- risks wiping out ocean wildlife and hurting the future of fishing communities in Europe, the groups said.

They found that bottom trawling currently took place in 77 percent of France's protected marine Natura 2000 sites, in 85 percent of Germany's and in 44 percent of Italy's.

"The joint complaint focuses on 15 marine Natura 2000 sites where extensive evidence shows bottom trawling continues unchecked on an industrial scale, damaging sensitive habitats such as reefs, seagrass beds, and sandbanks," the organisations said.

There is ongoing national legal action against the activities in France and Germany, and ClientEarth has taken similar action in the Netherlands and Spain.

Under EU law, the commission can assess the complaint and decide either to do nothing or open infringement proceedings against the member states concerned.

Although unlikely to lead to strong EU action, the complaint raises the issue ahead of next month's United Nations Ocean Conference in Nice, southeastern France.

"The complaint at the European level is a lengthy procedure, but it is a strategic lever to show the scale of the problem," said Marie Colombier of the Environmental Justice Foundation.

The EU has called on member states to phase out bottom fishing in all protected marine areas by 2030.

Europeche, which represents the interests of the EU fishing industry, said it "regrets" the complaint.

"The use of bottom trawls in marine protected areas (MPAs) must be assessed through site-specific impact studies," it said in a statement.

"Imposing the same bans everywhere would be tantamount to denying the complexity and diversity of marine protected areas," it said, and "would also have major consequences for our self-sufficiency and food sovereignty in Europe and France".