Mr Hammarstedt told Radio New Zealand this morning that his ship had been tracking the Thunder for 110 days since finding it fishing illegally in Antarctic waters.
Bob Barker was about half a mile away from the ship when it put out a distress call, and the crew began getting into life rafts.
The captain of the Thunder claimed it was struck by a cargo ship in the early hours of the morning.
He said when the Bob Barker arrived on the scene the Indonesian crew members appeared to have been taken by surprise by the sinking, but the officers on board had suitcases packed.
Mr Hammarstedt said he had no doubt the ship had been scuttled.
"We've been reporting to interpol and the Ministry of Primary Industries in New Zealand every day. They were at the end of their fuel and I'm confident that the captain of the Thunder thought he'd rather see the physical evidence that was on that vessel go down with that vessel."
The crew of the Thunder had been segregated from the Sam Simon's own 20 crew, because they had been violent towards the Sea Shepherd crews in the past.
He told Radio New Zealand the crew would be taken to the nearest port in the Gulf of Guinea and handed over to authorities.
No one was reported injured, according to Sea Shepherd.
The crew of the Thunder have been supplied with food and water, and will now be received by the Sam Simon.
Captain of the Sam Simon, Sid Chakravarty, said, "With the safety of my own crew also in mind, we will now take every precaution to ensure that the crew of the Thunder is retrieved from the lifeboats safely."
The Thunder is one of six vessels called the "bandit 6" by Sea Shepherd that are known to engage in illegal, unregulated, unreported fishing of vulnerable toothfish in the Southern Ocean.
