The three activists from Forest Rescue, an Australian group specializing in direct action to prevent logging, boarded the ship early on Sunday with assistance from the Sea Shepherd Conservation Society, Sea Shepherd said in a statement.
U.S.-based Sea Shepherd is tailing Japan's whaling fleet as it heads towards the Southern Ocean to try to prevent the cull.
The statement described the activists as "prisoners now detained on a Japanese whaler."
Speaking while en route to the Antarctic, Sea Shepherd founder Paul Watson told Reuters by satellite phone that the activists were still on board the Shonan Maru 2. He said the Japanese vessel had been sent to disrupt Sea Shepherd's longstanding campaign to stop the cull.
There had been no contact from the Japanese and the activists' radios appeared to have been seized, Watson said from aboard the Steve Irwin, one of two ships heading south with the aim of preventing the hunt from taking place.
"The Shonan Maru won't talk to us. They don't respond to our radio calls," Watson said. "They are chasing us."
A New Zealand-based spokesman for Japan's Institute of Cetacean Research, which coordinates the annual hunt, confirmed the three men were on the Japanese boat and uninjured. He did not rule out that they might be taken to Japan.
"The three men are on board," spokesman Glenn Inwood told Reuters. "They are being questioned now and they remain on the vessel."
The Japanese boat, he said, was 40 km (24.9 miles) off the Australian coast when the trio boarded it.
Forest Rescue spokesman Michael Montgomery had earlier said the action was to protest at inaction by the Australian government to stop the hunt and to demand the departure of the whalers from Australian waters.
"We don't need to kill these beautiful creatures any more," he told Reuters.
Sea Shepherd said the three activists came in a boat from Australia's western coast and approached the Shonan Maru 2 in the dark, with assistance from two Sea Shepherd boats.
"The three negotiated their way past the razor wire and spikes and over the rails of the Japanese whaling vessel," the statement said. "They are being held in Australian territorial waters by an invading Japanese vessel containing armed Japanese military personnel."
They carried with them a message reading: "Return us to shore in Australia and then remove yourself from our waters."
Whaling was banned under a 1986 moratorium, but Japan continues to hunt hundreds of whales annually under a loophole that allows whaling for "scientific" purposes.
(Editing by Ron Popeski)