Special Boat Service (SBS) operatives from Sabre Squadron fast-roped from helicopters on to the ship which had been sailing off the Thames Estuary, sources told Sky’s defence and security correspondent Alistair Bunkall.
The operation lasted around 25 minutes and no-one onboard was injured.
Essex Police confirmed the vessel will now be brought safely into dock at the Port of Tilbury and four men have been arrested under the Immigration Act.
Officers boarded the 236-metre long cargo ship, called the Grande Tema, shortly after 11pm on Friday.
The ship’s operator, Grimaldi Lines, had earlier reported that four stowaways armed with iron tubes had called for the crew to navigate closer to the coast.
The company’s spokesman Paul Kyprianou told Sky News: “The vessel was coming from Nigeria… They managed to escape from the cabin and started threatening the crew, requesting to have the vessel navigate very close to the coast.
“We understand they wanted to jump and reach the British coast.”
He added that the crew locked themselves in the bridge of the vessel after the migrants had picked up potentially harmful objects.
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“They managed to get whatever they could find on the vessel… pieces of iron, tubes and things like that and this is what they used in order to threaten,” Mr Kyprianou said.
“The vessel is under the command of the crew there is no question about that… the only problem is that we have four people who are free on the deck and they are threatening crew members and requesting they get close to the coast.”
The vessel had been travelling eastwards through the English Channel when the migrants were discovered on Friday morning.
Essex Police said they were not treating the incident as a “hostage, piracy or terror-related”.
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