The captain of an anti-whaling ship, which offered to help search for a Japanese whaling ship's missing crewman, rejects claims he continued to harass the whalers during the search.

The Sea Shepherd Conservation Society's ship Steve Irwin has been pursuing Japanese whaling ship Kyoshin Maru No 2 in an attempt to prevent it whaling.

Early on Monday morning Hajime Shirasaki, a 30-year-old engine room oiler, was reported missing from the Kyoshin Maru No 2 and is believed to have been washed overboard, and drowned, in Antarctic seas with four metre swells.

The Japanese ship claimed the Steve Irwin's harassment continued while it was searching for the missing man.

The Steve Irwin approached without its lights on and "began to harass and disrupt navigation", a statement said.

The statement said the Steve Irwin called the Japanese vessel and said it had "come to help in the search for the missing crewman".

The Japanese responded "we will not accept any help nor cooperation from the Sea Shepherd who has been harassing our research vessels".

The Dutch-registered ship replied "we will restart harassing the whaling vessels once the search is over".

Kazuo Yamamura, president of the Japanese ship's operator Kyodo Senpaku Kaisha, said the Steve Irwin disrupted the search.

"There is a distinctly uncaring nature about Sea Shepherd people in that they are prepared to disrupt the search for a missing seaman for their own ends."

Captain Paul Watson told NZPA it was "rude and unfair" for the Japanese ship to make such accusations.

"We told them very specifically that we were not there to harass them, that we respected their situation.

"So, I was rather shocked to hear that they said we were harassing them."

Mr Watson said the Japanese strategy was to demonise the anti-whalers.

"The fact is we're not breaking any laws. We haven't hurt anybody, we haven't damaged any equipment. But we have prevented them from killing whales.

"The biggest crime we've committed down here is saving lives."

The Japanese whaling fleet has not killed any whales since December 20 and Mr Watson is confident his teams efforts have reduced the number of whales killed and reduced the company's profits.

The Steve Irwin was returning to Hobart for refuelling and was being followed by a Japanese ship for the last 12 hours, Mr Watson said.

"As long as they're chasing us they're not killing any whales."

Maritime New Zealand's official search for the missing Japanese seaman has been called off.

NZPA