At least three dead whales have been spotted aboard a Japanese vessel in the Southern Ocean.

New Zealand's foreign minister condemned the whaling but disputed claims by conservation group Sea Shepherd that the fleet had been operating in New Zealand’s territorial waters, in the Ross Sea in Antarctica.

Murray McCully, foreign affairs minister, called the Japanese operation "pointless and offensive", adding: "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.'' Japan says the whale hunts are for scientific purposes.

Video shot by Sea Shepherd aircraft appears to show three minke whales loaded onto the deck of the factory ship, the Nisshin Maru. Activists say a fourth whale was being cut apart at the time of the filming, with crew members seen mopping up large pools of blood on the deck.

The organisation argues that Australia should enforce its own Antarctic territory by cracking down on whaling, which has been deemed unlawful by its federal court. However, only four countries – which do not include Japan – recognise Australia’s claim to Antarctic land and sea territory.

Sea Shepherd said the Japanese fleet fled out of the whale sanctuary without violent confrontation. There was no sign of either the HMNZS Otago, which is patrolling New Zealand’s southern waters during whaling season, nor an Australian government aircraft, which was put forward by the country's environment minister Greg Hunt in lieu of the customs vessel he promised before the election.

Jeff Hansen, the managing director of Sea Shepherd Australia, told Guardian Australia that the Japanese fleet was “on the run”.

“We are keeping on their tail and they aren’t whaling at the moment so we’re happy about that, at least,” he said. “There is no need for confrontation, the number one priority is the protection of whales.”

Hansen said the minke whales killed could include some that were tagged by Australian scientists last year to measure their progress from the Great Barrier Reef down the east coast to Victoria.

Separately, 39 pilot whales were stranded overnight at Farewell Spit in New Zealand, with twelve dying initially and the remaining 27 being euthanised by authorities who said they could not be saved.

John Mason, Golden Bay Conservation Services Manager, said: "We carefully weighed up the likelihood of being able to refloat them and get them safely back out to sea. But our staff, who have extensive experience in dealing with mass whale strandings in Golden Bay, determined that due to various factors it was unlikely they could be rescued."