The Japanese whalers had accused the pair of attacking their vessel with bottles of acid and boarding their ship illegally, although later Japanese officials said they found no damage to their vessel.
But later efforts to arrange a handover of the two men degenerated into a stand-off, with both sides blaming the other for the delays and trading accusations of piracy.
Japanese officials said the whaling fleet had told the Sea Shepherd ship to come and pick up its two activists, and issued safety instructions for the hand-over.
For its part Sea Shepherd founder Paul Watson said the whalers were demanding that the group end its harassment of the whaling fleet as a condition of securing the pair's freedom.
|The Steve Irwin has been chasing the whalers |
for several weeks [Photo: Sea Shepherd]
Australia meanwhile criticised both sides for behaving in a potentially dangerous way in a region that is thousands of kilometre from the nearest help.
Hoping to tame a growing diplomatic row Stephen Smith, Australia's foreign minister said he had called on both sides to cooperate "to ensure we get a safe and speedy transfer of the two gentlemen".
"From the very first day I urged all parties in this matter to exercise restraint," Smith told ABC radio. "It is quite clearly the case that restraint hasn't occurred here."
The incident late on Tuesday dramatically raised tensions in the Southern Ocean as the Japanese fleet looks to continue its annual whale hunt.
On Wednesday the Japanese government defended its sailors actions against the activists.
"What they did was extremely dangerous"
Nobutaka Machimura, Japan's cabinet secretary
"What they did was extremely dangerous," Nobutaka Machimura, Japan's cabinet secretary, told reporters. "And as the Japanese government we strongly condemn these acts."
Sea Shepherd's ship, the Steve Irwin - named after the late Australian wildlife television presenter - has been tracking the Japanese whaling fleet for several weeks hoping to disrupt the hunt.
The group said that after being detained activists Benjamin Potts, an Australian, and Giles Lane, a Briton, were tied to a radar mast and dunked in icy water before being taken below deck, claims the Japanese have denied.
The Sea Shepherd also said the activists only threw stink bombs of rancid butter, and not acid, onto the decks of the whaling ship.
Paul Watson, skipper of the Steve Irwin, told Australian television the two men had boarded what he called a poaching vessel "that's involved in highly illegal activities, taking endangered species in a whale sanctuary, and we're just simply trying to enforce the law".
Sea Sheperd has a reputation for pushing the boundaries of peaceful protest over whaling and has in the past rammed Japanese whalers.
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 are research over the Antarctic summer.
It earlier abandoned plans to cull 50 humpback whales following international condemnation and a formal protest by 31 countries.