The Melbourne-based crew of the Bob Barker responded to a distress signal from the pirate fishing vessel the Thunder, the very ship they had been chasing for the past 110 days.

Speaking on a satellite phone from the deck of the Bob Barker, Captain Peter Hammarstedt said he received the mayday signal about 6am local time on Monday and immediately responded to the call.

"We sent out our own crew to assist straight away. It was clear the ship was sinking," Captain Hemmarstedt said.

"It's a very unusual rescue situation. We will need to activate our security plan and proceed very carefully, but we have a responsibility under international law to take them onboard," he said.

The Thunder, under investigation by Interpol and suspected of poaching tens of millions of dollars worth of toothfish, was discovered by the Bob Barker off the coast of Antarctica over three months ago, dumped its illegal gill nets and took off, Captain Hammarstedt said.

The Sea Shepherd had made numerous reports to transnational authorities claiming the Thunder had repeatedly tried to ram the Bob Barker and hurled grappling hooks and other metal projectiles at the vessel during the long pursuit.

At 11am local time there were three life rafts in the water carrying all 40 of the pirate vessel's crew members, Captain Hammarstedt said.

A second Sea Shepherd vessel, the Sam Simon, was also on the scene and preparing to take on the crew.

Captain Hammarstedt suspected the crew, knowing they were running low on fuel, had deliberately tried to sink their ship in order to be picked up by the Nigerian Coast Guard.

"We believe they were trying to sink the ship to get rid of the evidence [of illegal fishing]," Captain Hammarstedt said.

Three Bob Barker crew members who boarded the vessel once it had been evacuated found the ship's hatches had been left open, allowing the ship's compartments to flood as it sank.

"Generally if your ship is sinking you'd try to close off compartments to maintain buoyancy but they did the opposite," Captain Hammarstedt said.

While onboard the sinking ship the Bob Barker crew confiscated mobile phones and computers to turn over to authorities as evidence of illegal fishing.

The captain of the Thunder had been in radio communication with the Bob Barker but had refused to give his name.

"I don't think he's terribly happy to be rescued by us," Captain Hammarstedt said.

The Maritime Rescue Coordination Centre in Nigeria had requested the Sea Shepherd vessel take charge of the rescue operation, and had put a call out to commercial shipping and naval resources to render assistance.