Three whaling activists have been transferred from a Japanese vessel to an Australian customs ship.

Attorney-General Nicola Roxon issued a statement this evening confirming the transfer to the ACV Ocean Protector, which she said came at "great expense to the Australian taxpayer.

"The transfer of the Australians was conducted using the tenders from the ACV Ocean Protector approaching the Shonan Maru No. 2. The transfer process took place with full cooperation from all parties," the statement said.

"The men are reported to be in good health, but all will be assessed by medical staff onboard the ACV Ocean Protector."

Ms Roxon said she hoped the men would reflect on their actions.

"We support peaceful protest, but dangerous action on the high seas is quite different. We strongly encourage both sides of this dispute to respect the law and act calmly," she said.

"Protestors must be aware that, in the future, such action may lead to charges in another country and possible conviction."