The move comes after Westminster voted down an amendment to the Fisheries Bill which would have committed them to banning supertrawlers from marine protected areas after the UK leaves the Common Fisheries Policy early next year.
The 117m-long boat, which is registered in Germany, was intercepted by campaign group Greenpeace while fishing legally in the Central Fladen protected area, in the northern North Sea.
The campaigners informed the skipper that the crew were fishing in a protected area and requested they stop.
When the plea was refused, activists climbed aboard the vessel and unfurled a banner reading ‘Ban supertrawlers now’.
The Greenpeace team then approached with fishing deterrents to place in the supertrawler’s nets, at which point the vessel moved on.
“Supertrawlers have no place in our protected areas,” said Greenpeace UK oceans campaigner Chris Thorne, who was part of the protest team.
“What use is a protected area when the highest-intensity industrial fishing vessels are allowed to operate inside it?
“Regardless of whether a protected area protects the seabed or marine life like porpoises which are directly threatened by supertrawlers, the operations of a supertrawler in a supposedly protected area make a mockery of the word protected.”
Greenpeace investigations have revealed that the amount of time supertrawlers spend fishing in UK protected areas has doubled every year since 2017, racking up the equivalent of 232 entire days already this year.
The massive vessels can catch hundreds of tonnes of fish each day in nets up to a mile long.
Mr Thorne added: “Our government refuses to act so we’ve been forced to step in.
“We have stopped this destructive industrial vessel from fishing in one of our protected areas for as long as we can.
“We can’t stop it permanently – that’s up to our government.”
The Central Fladen protected area safeguards the seabed.
Although the seabed may escape damage by the supertrawler, environmentalists say the massive catches landed by such vessels on a daily basis will impact the entire marine ecosystem.
Research has demonstrated that fish stocks both inside and outside a protected area are significantly boosted when destructive fishing is prohibited.
More than 80 MPs from all political parties have written to environment secretary George Eustice, calling for a ban.
Labour will table another amendment to the Fisheries Bill this afternoon which would commit the government to banning supertrawlers from fishing in UK protected areas after Britain leaves the Common Fisheries Policy.
Greenpeace is calling for all offshore marine protected areas to be put off limits to industrial fishing, beginning with the highest-impact vessels like supertrawlers and bottom-trawlers.
Sustainable fisheries campaigners have criticised Scottish ministers for the “free-for-all” that allows damaging fishing in ecologically sensitive areas.
Phil Taylor, head of policy at sustainable seafood charity Open Seas, said: “Sadly this is just another example in a long list of mismanagement of Scotland’s seas and undermines the reputation of Scotland’s seafood.”
He says marine protected areas – and Scotland’s whole coastal zone – need proper protection.
“These areas are vital for the health of our marine ecosystems and fishing methods that cause widespread damage need prohibited there,” he said.
“The government needs to end the current free-for-all by urgently implementing measures.”
He added: “Fishing quotas have been sucked up by a few very big commercial operations, some operating supertrawlers like these.
“These companies exploit our publicly owned seas and fish but give very little back to our economy and communities.
“The current quota system needs reformed to incentivise coastal seafood businesses who deliver in Scotland’s best interests.”