"Captain Bethune boarded a Japanese whaling fleet security ship at high speed in total darkness, breached the spikes and anti-boarding nets and is presently onboard," he said.
In Japan, a spokesman for the fisheries agency later confirmed that an activist had boarded the ship.
"He is now in Japanese custody. It is not an arrest. Under existing laws, the captain can take measures as he considers necessary," the spokesman said.
"Nothing is really happening. The man is not being belligerent."
Ady Gill sinking
Sea Shepherd said Bethune had been planning to arrest the Shonan Maru No. 2's captain for "the destruction of the Ady Gil and attempted murder of the six Ady Gil crewmembers".
Last month, the Japanese vessel struck the Ady Gil, a high-tech speed boat run by Sea Shepherd, sinking it in Antarctic waters.
Sea Shepherd said that Bethune would also attempt to hand over a $3m bill for the destruction of the Ady Gil.
"Sea Shepherd anticipates that the Japanese will hold Captain Bethune as prisoner onboard the Shonan Maru 2," the group's statement added.
The Sea Shepherd activists claim to have saved the lives of hundreds of whales by harassing the annual hunt, which kills the animals using a loophole in an international moratorium which allows "lethal research".
Australia and New Zealand have called for restraint from both sides in their Antarctic clashes, with the activists deploying laser-like devices and stink bombs and the Japanese fleet operating military-style acoustic weapons.