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The resumption of so-called "scientific'' whaling in the Southern Ocean has been condemned by Foreign Affairs Minister Murray McCully.
Anti-whaling group Sea Shepherd said it was pursuing the Japanese fleet after finding all five of its vessels in the Southern Ocean, along with evidence of whale kills.
The Sea Shepherd fleet, comprising the Steve Irwin, the Bob Barker and the Sam Simon, was now trailing the Japanese ships in a bid to disrupt or shut down their whale-killing operations.
The Steve Irwin's helicopter first spotted the Japanese vessel, Nisshin Maru, in what the organisation said was New Zealand's sovereign waters in the Ross Dependency Antarctic region and inside the internationally recognised Southern Ocean Whale Sanctuary.
The Sea Shepherd group said it had footage of three dead protected minke whales on the deck of the Nisshin Maru, taken when the factory ship was first found.
A fourth whale, also believed to be a minke, was being butchered on the deck.
Mr McCully said reports by Sea Shepherd that whaling occurred in New Zealand sovereign waters were factually wrong.
"New Zealand has responsibility for co-ordinating search and rescue operations in a large area in the Southern Ocean, however these are international waters and not within New Zealand's maritime jurisdiction.''
However, today's information suggested the Japanese fleet had commenced whaling for the season, he said.
"The practice of whaling in the oceans south of New Zealand is pointless and offensive to a great many New Zealanders.
"The New Zealand Government has repeatedly called on Japan to end its whaling programme. We reiterate this message today,'' Mr McCully said in a statement.
New Zealand formally lodged an intervention before the International Court of Justice in the case brought by Australia against Japanese whaling in the Southern Ocean. A judgment in the case is yet to be delivered.
The Sea Shepherd group said its fleet would do what it could to ensure no more whales suffered at the hands of the Japanese.
"Sea Shepherd will remain relentless in driving these fake, desperate and subverting `scientists' back to Tokyo,'' the Steve Irwin's captain, Sid Chakravarty, said.