Australian Benjamin Potts, 28, and Briton Giles Lane, 35, boarded the Yushin Maru No. 2 after chasing it in a rubber boat and were tied up on deck while other Sea Shepherd activists threw bottles of acid onto the deck, Japanese officials said.
Watson said the activists wanted to deliver a letter demanding an end to the whale hunt and then leave, but were roughed up and held against their will.
Australian Foreign Minister Stephen Smith said Australian officials had twice contacted their Japanese counterparts to press for the release of the two activists, and were assured this would happen.
He urged both sides to work together to bring about the "safe and speedy" return of the men to the Steve Irwin.
"From the very first day, I urged all parties in this matter to exercise restraint," Smith told ABC radio, referring to previously known plans for the environmentalists to chase the whalers. "It's quite clearly the case that restraint hasn't occurred here."
He warned later at a news conference: "We're dealing with the great distance of the Southern Ocean. The capacity for adverse incidents is high, and the capacity for rescue or assistance is low."
"Hostages" and "Pirates"
In Tokyo, Japanese Fisheries Agency official Takahide Naruko told reporters the whalers decided to release the activists because they had done no damage to the ship, but Sea Shepherd had not responded to efforts to arrange the handover.
Whaling has been halted until the two are handed over, Naruko said.
Hideki Moronuki, a spokesman for the Japanese Fisheries Agency's whaling section, said it sent safety instructions for the hand-over, but attached no further conditions in terms of Sea Shepherd's activities.
But Watson said Japan was demanding Sea Shepherd stop harassing, filming, or photographing the whalers, and that the transfer of the pair be conducted by small boat, 10 nautical miles (18.5 kilometers) from the Yushin Maru.
"I find it very strange that people who are holding hostages are calling us the pirates," Watson said.
Laws and Customs
The event was a rapid escalation of the annual contest between the fleet that carries out Japan's controversial whale hunt in the ocean at the bottom of the world and the environmental groups that try to stop them.
Smith said Australian Federal Police were evaluating whether any laws had been broken.
Naruko said whalers briefly tied up the two activists near the bridge of the Yushin Maru and later moved them to a cabin.
Japan sent ships to Antarctica in November to kill about 1,000 whales under a program that skirts an international moratorium on whaling because Tokyo says the kill is for scientific purposes. The program is widely condemned as a front for commercial whaling.
Under intense international pressure, Japan abandoned its plans to include 50 humpback whales in this season's hunt, which is due to run until April.
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Associated Press writers Rohan Sullivan in Sydney and Mari Yamaguchi in Tokyo contributed to this report.
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