Campaigners targeted the 117m-long Helen Mary which they claimed was fishing in the Central Fladen marine protected area, east of Scotland.
Climbers boarded the vessel and dropped a banner reading “Ban supertrawlers now”.
Activists onboard the Greenpeace ship Esperanza then approached the fishing vessel with deterrents to place in the supertrawler’s nets, at which point Helen Mary left the area, Greenpeace said.
In 2019, the same vessel was detained at sea by Marine Scotland on suspected fishery offences.
The ship is owned by Netherlands-based fisheries company Parlevliet & Van der Plas, which said the vessel was detained briefly in 2019 but released the same day without penalty.
The Independent contacted Parlevliet & Van der Plas for comment. In a response from the Pelagic Freezer-trawler Association, of which Parlevliet & Van der Plas is a member, the group said: "These vessels were operating entirely legally. Greenpeace's campaign peddles mistruths and ignores the scientific basis for MPAs (Marine Protected Areas).
"After decades of collaboration with governments and the scientific community the processes pelagic fishing has in place ensure we are fishing sustainably."
Supertrawlers are high intensity fishing vessels, measuring more than 100m in length and capable of catching hundreds of tonnes of fish each day using nets up to a mile long. They are particularly controversial because the size of their nets mean their bycatch can include dolphins, porpoises and seals.
The Central Fladen marine protected area lies within the Fladen Grounds, a large area of mud in the northern North Sea.
The area includes a mud habitat home to soft corals called sea pens and burrows made by crustaceans such as mud shrimp and the Norway lobster.
Chris Thorne, a Greenpeace UK oceans campaigner on board the Esperanza ship, said: “Supertrawlers have no place in our protected areas. 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.
“Every year since 2016, supertrawlers have doubled the time they’ve spent fishing in our protected areas. 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. They could announce a ban on destructive industrial vessels fishing in our protected areas tomorrow. They must act.”
Greenpeace said they carried out investigations which revealed supertrawlers had doubled their time spent fishing in UK protected areas every year since 2017.
So far in 2020, supertrawlers have already spent more than 5590 hours – equivalent to 232 entire days fishing time – in UK protected areas, the organisation claimed.