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.