The Steve Irwin and the Bob Barker put to sea last year with the express intention of disrupting the whaling season.
A police spokesman said the searches were a response to "a formal referral from Japanese authorities." He would not say whether anything had been seized.
The Ady Gil, which made up the trio of Sea Shepherd vessels, was holed in a clash with the Japanese and sank.
Peter Bethune, the New Zealander who captained the Ady Gil, is being held aboard one of the Japanese vessels after he leapt aboard to deliver a bill for the loss of the super-fast trimaran.
Greens leader Bob Brown, who was among well-wishers at the dockside, accused the police of siding with the Japanese.
"This is outrageous that Australian police are at the disposal of the Japanese whale killers," Brown said.
Japan uses a loophole in the 1986 whaling moratorium to continue catching whales under the guise of scientific research.
Canberra has promised to take legal action in an international court by November if Japan does not stop whaling. Tokyo is standing firm, noting that whaling is allowed by the International Whaling Commission and promising to defend itself in the courts.
The Japanese government has also promised to put Bethune on trial for piracy when the whaling fleet returns to port later this month.
Sea Shepherd founder Paul Watson said log books, videos, photographs, charts and GPS recordings had been taken along with copies of computer hard drives.
"The Japanese deliberately rammed and destroyed one of our ships and almost killed six of our people but nobody's questioning them, so it seems to be very one-sided," Watson told Australia's AAP news agency.