The New Zealand Embassy staff in Tokyo met with New Zealand's anti-whaling protestor Peter Bethune Friday night, Foreign Minister Murray McCully said on Saturday.

"Consular officials are providing updates on Bethune's situation to his wife as they become available. Embassy staff report he is well and continues to be in good spirits," McCully said in a statement.

Bethune has been arrested and charged with trespass. He has legal representation and was due to meet his lawyer.

The anti-whaling group Sea Shepherd said the arrest of protester Peter Bethune in Japan is ridiculous, and the group will stand by him and help with his defence.

Bethune was arrested on Thursday after being taken to Tokyo by the whaling research vessel Shonan Maru II, which he had boarded three weeks ago in an attempt to make a citizen's arrest for what he said was the attempted murder of his crew.

Instead he was taken into custody and transported to Japan.

The Shonan Maru II was involved in a collision with the protest boat Ady Gil in the Southern Ocean two months ago.

Sea Shepherd's Paul Watson said the Japanese skipper, not Mr Bethune, should have been arrested. He says the Japanese ship destroyed the Ady Gil and almost killed six people, yet has escaped without a reprimand.

The group said it has four lawyers in Tokyo who can work with Mr Bethune.

A spokesperson for Japanese whaling, Glen Inwood from the Institute of Cetacean Research, said he doesn't expect any leniency from the Japanese authorities.