The Oceanic Viking is on a mission to collect evidence that might be used in international courts to prove that the Japanese programme, which Tokyo says is for research, is a front for commercial whaling.
Paul Watson, founder of the Sea Shepherd, said the two men were safely back on board the group's ship, the Steve Irwin.
"We have got them back without any conditions and now we are going to continue on harassing and chasing the Japanese fleet," he said.
Glen Inwood, a spokesman for the Institute of Cetacean Research which oversees Japan's whaling programme, told New Zealand radio o
n Friday that the fleet would now resume hunting.
Whaling operations had been halted since Tuesday when the two activists boarded the Japanese harpoon ship.
Bob Debus, Australia's home minister, told Australian Broadcasting Corp radio that it had "been important, I believe, that we have been there and able to assist in resolving this difficult situation".
The whalers and conservationists had accused each other of behaving like terrorists, with Japan calling the boarding of the boat an act of "piracy" and Sea Shepherd saying the men were being held as "hostages".
Japanese officials had said they were prepared to release the activists if Sea Shepherd had promised not to attack the whaling boat during the transfer and if the Steve Irwin stayed 10 nautical miles clear of the Yushin Maru 2, using a small rubber zodiac boat instead.
|The two sides had accused the other |
of acting like terrorists [AFP]
But Watson, who is also captain of the Steve Irwin, had rejected the conditions, demanding an "unconditional" release and threatening to launch more protest action if the transfer was made directly to his ship.
The row over the activists had dramatically raised tensions in the annual battle to stop Japan from hunting whales.
Sea Shepherd has said it will do everything it can to block the hunt and has a reputation for pushing the boundaries of peaceful protest over whaling, having used its ship to physically ram Japanese whalers in the past.
The group says its actions are intended to disrupt the hunt and are aimed only at disabling equipment, but critics say such actions put human life at risk as well, especially in the inhospitable Antarctic environment.
Japan plans to hunt almost 1,000 minke and fin whales for what it says is research over the Antarctic summer.
Last year it announced it was abandoning plans to cull 50 humpback whales following international condemnation and a formal protest by 31 countries.