The captain of an alleged pirate ship accused of fishing illegally in Antarctic waters clapped and cheered as his vessel sank off the West African coast overnight, an indication that the ship had been deliberately scuttled, according to Sea Shepherd activists.

In what was described as a "weird and surreal" experience, Sea Shepherd crew members have now rescued 40 people from the alleged poaching vessel, the Thunder, which the conservation group had been pursuing for nearly four months from the Southern to the Indian and Atlantic oceans.

Captain Peter Hammarstedt, the director of ship operations for Sea Shepherd Australia, told Fairfax Media from the deck of the Bob Barker, a Sea Shepherd vessel, that the Nigerian-flagged Thunder was now "3800 metres below the surface of the sea".

Crew members from the Thunder had been towed on life rafts to the Bob Barker's sister ship, Sam Simon, where they were being given food, water and medical attention before being taken to Sao Tome, in the Gulf of Guinea, where the crew would be handed over to local law enforcement authorities