New Zealand anti-whaling activist Pete Bethune has been arrested after his Japanese captors delivered him to customs officials in Tokyo Harbour this afternoon.

Bethune was the Sea Shepherd skipper of the sunken boat the Ady Gil when he tried to board a Japanese whaling ship last month to arrest its captain for ramming his boat.

Authorities in Japan are now expected to spend the next few days deciding whether to charge Bethune with offences which carry a potential jail term.

The Minister for Agriculture, Forestry and Fisheries, Hirotaka Akamatsu, has sent out a clear message to the world about its right to continue whaling in international waters.

"A person who did something bad should be strictly punished following the law," he said.

The chief cabinet secretary, Hirofumi Hirano, also spoke publicly, even before the arrest had been officially made.

"I don't think this will deteriorate our relationship with Australia," he said.

Soon afterwards, Japanese media helicopters caught a glimpse of Bethune with a blue sheet covering his face, back on dry land in Tokyo Harbour.

Coast guard officers escorted him away from the Shonan Maru 2. Later in a media conference, the officials said that Bethune nodded and accepted his arrest without protesting.

They also revealed that New Zealand consular officials and his lawyers would be able to visit him in custody soon.

Back in his home town of Hamilton, Bethune's family was angry and upset.

Mary Russell Bethune says her stepson has been out of contact for a month.

She says he was in contact with his wife on Valentine's Day, but that was the last contact the family has had with him.

"You imagine putting yourself in my shoes and seeing how you feel," she said.

"It's a terrible, worrying concern and we just hope that Sea Shepherd and the New Zealand and Australian governments are going to be able to step in and be able to do something to help Pete."

Her husband and Pete Bethune's father, Don, says his son is prepared to pay a price for his principles.

But Mr Bethune says his son is not easily frightened by discomfort or risk.

"If it was necessary he would [go to jail], there'd be no squealing from him. One might say he takes what society decides to give him," he said.

Japan's whaling fleet is operated by the Institute of Cetacean research. Its New Zealand spokesman, Glen Inwood, thinks the Japanese public want the government to take a hard line against Bethune.

"They want these people dealt with because they're tired of Japanese people being put at risk by the actions of this," he said.

"Really Japan's whaling is purely legal which means that anything Sea Shepherd does is purely illegal."