Japan's new fisheries minister has vowed that his country will never stop hunting whales, comparing eating the ocean-going giants to Australians' consumption of kangaroos.

In an interview with the AFP news agency, Yoshimasa Hayashi said criticism of the practice is "a cultural attack, a kind of prejudice against Japanese culture".

Japan's so-called scientific whaling program has been criticised by other nations, including Australia, and the country's whaling fleet is currently clashing with Sea Shepherd activists in the Southern Ocean.

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Japan says it needs to kill whales for research reasons, but Mr Hayashi did not make any mention of the scientific rationale behind the program during the AFP interview.

Instead, he said that eating whale meat was an integral part of Japanese culture, and pleaded for other nations to respect Japanese tradition.

"I don't think there will be any kind of an end for whaling by Japan," Mr Hayashi, who was handed oversight of the country's whaling programs in December, said.

"Japan is an island nation surrounded by the sea, so taking some good protein from the ocean is very important. For food security I think it's very important.

"We have never said everybody should eat whale, but we have a long tradition and culture of whaling.

"So why don't we at least agree to disagree? We have this culture and you don't have that culture.

"In some countries they eat dogs, like Korea. In Australia they eat kangaroos.

"We don't eat those animals, but we don't stop them from doing that because we understand that's their culture.

"Whaling has long been part of traditional Japanese culture, so I just would like to say 'please understand this is our culture'."

Japan's fleet is struggling to catch any whales during this year's Antarctic hunt because of constant harassment by the Sea Shepherd conservation group.

Opinion polls suggest only 5 per cent of Japanese people regularly eat whale meat, and the ABC understands that there could be up to 6,000 tonnes of whale sitting unused, unsold and unwanted in freezers around Japan.

Military 'intimidation'

Meanwhile, Sea Shepherd has accused the Japanese government of using a military ship to intimidate their activists who are trying to stop the whale cull in Australian Antarctic waters.

The anti-whaling ship Bob Barker was involved in a dramatic crash with the Japanese whaling ship the Nishhin Maru on Monday night.

Both parties blame the other for the crash.

Sea Shepherd founder Paul Watson says a 12,000-tonne Japanese military ship, the Shirase, is in the area and is providing support for the whalers.

"Japan is saying it's just down here doing independent research, but that research seems to involve monitoring us and dropping commandos onto the tanker," he said.

Federal Environment Minister Tony Burke says the ship has conducted genuine research in the past, and he has sought urgent confirmation from the Japanese government on the Shirase's involvement.

ABC/AFP