Japan's foreign minister says an anti-whaling activist being held onboard a Japanese whaling vessel in the Antarctic Ocean will be taken to Tokyo and will not be released to a third country.

Foreign Minister Katsuya Okada says Peter Bethune, from the Sea Shepherd conservation group, is being held aboard the ship under international maritime law.

"In principle we will not hand the activist over to a third country. We are preparing to bring him to Japan," he said. "He is under protective custody in accordance with the law."

Mr Bethune was detained two days ago after jumping aboard the Shonan Maru 2 and attempting to present its skipper with a $3 million bill for the destruction of the Ady Gil powerboat, of which he was captain.

Japanese media reports say that after Mr Bethune has been taken to Tokyo, the government will try to establish a criminal case and possibly charge him with piracy.

Japan's NHK television is reporting that the New Zealander will be detained on the Shonan Maru 2, the security ship shadowing the Japanese whaling fleet in the Antarctic.

"Bethune is to be handed over to the Japan Coast Guard when the ship returns to Japan in about a month, and could face charges under Japanese law," the report said.

"Bethune would be the first Sea Shepherd member to be questioned by Japanese authorities."

Mr Okada will visit Australia this weekend for talks with Prime Minister Kevin Rudd and his foreign and defence ministers, and Japan's whaling program is again expected to be high on the agenda.

"We are going to discuss various bilateral issues as well as global issues such as climate change and nuclear disarmament, to develop a strategic partnership between our two countries," said Mr Okada.

"Probably we will discuss [the] whaling issue as well. Australia has various opinions about research whaling. So we discuss these sufficiently" he says.

While threatening legal action against Japan over its whaling program, Prime Minister Kevin Rudd has insisted he will try to find a diplomatic solution first.

Two years ago two Sea Shepherd activists boarded a whaling ship and tied themselves to the deck, but they were later released with the help of an Australian government ship.