In their complaint, the organisations including Environmental Justice Foundation and ClientEarth, accused the three EU 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, seriously damaging ecosystems in the process -- risks wiping out ocean wildlife and hurting the future of fishing communities in Europe, the groups warned.

They found 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 sites.

"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 in France and Germany. ClientEarth has taken similar action in The Netherlands and Spain.

Under EU law, the commission can assess the complaint and either decide to do nothing or launch 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 calls on member states to phase out bottom fishing in all marine protected areas by 2030.