Anti-whaling activists in the Southern Ocean have not ruled out boarding and disabling a Japanese whaling vessel to recover two crewmates held by the whaling crew since Tuesday.

Australian Benjamin Potts, 28, and Briton Giles Lane, 35, have been detained on board the Yushin Maru No 2 since late on Tuesday afternoon after boarding the harpoon boat from Sea Shepherd Conservation Society's ship, the Steve Irwin.

Captain of the Steve Irwin Paul Watson said his ship was pursuing the Japanese whaling ship holding his two crewmen.

Captain Watson would not disclose Sea Shepherd's tactics if his ship caught the whaler, which is about 70km in front outside Australian waters in the Southern Ocean, more than 4,000km south-west of Fremantle.

"We will try and do everything we can to stop them killing whales. That's what we are doing down here," Captain Watson told AAP.

"We don't divulge our tactics until we do them but over the last 30 years we have shut down dozens and dozens of illegal whaling operations. We have never been convicted of a crime and we have never injured anybody.

But when asked directly if their action could involve once again boarding the Yushin Maru No 2, he said: "That's always a possibility. We board poaching vessels all the time, especially shark-finners off Guatemala, the Galapagos, Costa Rica. We have boarded probably 65 different poaching vessels and disabled them."

Morale is high on the Steve Irwin despite the events, Captain Watson said.

"We're all feeling pretty good because of the fact that they haven't killed any whales for six days and it looks like we can stop them for another six to 10 days, so that is a good thing, and I'll bet the guys on board the Japanese whaler are feeling pretty good about that too," he said.

"We're chasing them and they can't whale, so we are keeping them on the run."

Foreign Minister Stephen Smith said the two governments had struck a deal to have the men returned to the Steve Irwin and called for cooperation between the captains of the two vessels.

But Japanese Fisheries Agency's chief of whaling Hideki Moronuki said the pair would not be released unless the Sea Shepherd boat agreed to a set of conditions.

According to Sea Shepherd, they include agreeing not to take any action against the whaling activities, including filming or photographing the hunt.

But Mr Watson demanded international action to recover his crewmen.

"All I know is that if I was down here holding Japanese whalers hostage and making demands there would be all hell to pay, so I can't understand how these guys can come down here, engage in criminal activity like plundering endangered species in a whale sanctuary, and get away with abduction, kidnapping and extortion."