The Australian government offered a solution to the standoff, announcing Thursday it will send a ship to retrieve the men and return them to their anti-whaling vessel as soon as the details can be arranged.
The faceoff over the activists has escalated the annual contest between the fleet that carries out Japan's controversial whale hunt in southern waters and the environmentalist groups that try to stop it.
The founder of the Sea Shepherd anti-whaling group, Paul Watson, told The Associated Press by satellite phone that the Japanese are targeting vulnerable whale stocks and said his organization will keep harassing the fleet.
"We will chase them until they stop their hunt," Watson said from the bridge of the Steve Irwin, a Sea Shepherd vessel. "As long as we are chasing them, they aren't killing whales."
Japanese officials said a Greenpeace boat also was shadowing the whaling fleet.
Watson claimed the two activists were being held as "hostages" on the Japanese harpoon ship Yushin Maru 2, but no Sea Shepherd boat had been sent to retrieve them.
Japan condemned the incident, calling the boarding of harpoon boat an act of "piracy" and accusing Sea Shepherd of stalling a handover of the activists to get publicity.
"These people aren't hostages, they're unwanted guests," Japanese Foreign Ministry spokesman Tomohiko Taniguchi said, adding Japan wanted to hand them off as soon as possible.
The announcement of the Australian ship came hours after Hideki Moronuki, a spokesman for the Japanese Fisheries Agency's whaling section, said his country was contacting the Australian government for help in arranging the return of the men.
Japanese officials said Sea Shepherd must agree not to attack the whaling vessel during any rendezvous to turn over the two protesters. Watson refused to comply, demanding an "unconditional" release.
"When people hold hostages and make demands, that's the behavior of a terrorist organization," he said. "I'm not going to acquiesce to their demands."
Australian Foreign Minister Stephen Smith called for caution on both sides.
"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," he said.
An official at the Japanese Fisheries Agency, Takahide Naruko, said the fleet would not resume its planned hunt of about 1,000 whales until the activists were handed over. He said there was "no telling what Sea Shepherd would do" if the fleet hunted with the activists on board.
Sea Shepherd protesters earlier attacked the harpoon ship with bottles of acid and tried to entangle its propellers, both Japanese officials and Watson said.
Watson claimed the two activists were not involved in throwing the acid and said they intended only to board the ship to deliver a protest letter.
The men were detained and briefly tied up. Watson alleged the Japanese crew assaulted the activists, which Japanese officials denied.
"It is completely illegal to board anyone's vessel ... on the high seas," said Glenn Inwood, a spokesman for Japan's Institute for Cetacean Research, which organizes the hunt. "So this can be seen as nothing more than an act of piracy by the Sea Shepherd group."
Japan sent ships to Antarctica in November to kill minke and fin whales under a program that skirts an international moratorium on commercial whaling.
The ban allows limited hunts for scientific research, a loophole Japan has used to kill nearly 10,000 whales over the past two decades, according to the International Fund for Animal Welfare.
Opponents say Japan's program is commercial whaling in disguise because the meat is later sold on the market. Environmentalists say Japan's hunts are detrimental to vulnerable whale populations in the area.
Japan's top government spokesman defended the catch.
"The activists are obstructing what are legal activities in international waters, and in an extremely dangerous way," Nobutaka Machimura said. "Japan strongly condemns these actions."
The whaling fleet's mother ship, the Nisshin Maru, has been chased 435 miles from the standoff scene by a boat belonging to the environmental group Greenpeace, Japanese officials said.
Despite the disruptions, Japan has no intention of calling off the hunt, said Taniguchi, the Foreign Ministry spokesman.
"It's clear the situation is very grave," he said. "But I can tell you, Japan has no plans to quit."