SYDNEY (AFP) – Militant activists seeking to cripple Japan's Southern Ocean whaling campaign on Wednesday said they had tracked down and were chasing a factory ship key to the Antarctic harpoon mission.

A vessel from the Sea Shepherd Conservation Society found the Nisshin Maru late Tuesday in the ice of the Ross Sea after a 26-day pursuit covering 4,000 nautical miles (7,400 kilometres), striking a blow to the Japanese fleet.

"We found it yesterday and it had just started whaling again, so we know they killed one whale," activist Captain Paul Watson told AFP by satellite phone.

"But they're now running from us and running full speed so they're not whaling today, that's for sure."

Sea Shepherd used weather balloons fitted with radar to zero in on the "serial killing death ship", which slipped away from the activists when they first found the Japanese fleet on December 31, he added.

Japan's fisheries agency told AFP the activists had dispatched a "helicopter to chase our ships" but that there were no reports of damage or injury as a result of their activities.

"We cannot comment on whether their activities are actually affecting our work," said fisheries spokesman Shigeki Takaya.

"We have no change in our plan. We are going to pursue it as scheduled."

While searching for the Nisshin Maru, Watson said his boats -- the Steve Irwin, Bob Barker and superfast interceptor craft Gojira -- were followed by two of the three Japanese harpoon ships, which prevented them from spearing whales for more than three weeks.

Sea Shepherd also found and intercepted the fleet's refuelling and supply ship, the South Korean-owned Sun Laurel, Watson alleged, in another blow to the Japanese mission.

"This has been our most successful year so far. We found the whaling fleet before it even begun to kill whales and I don't think they've taken very many whales at all," said Watson.

"We've had two of their three harpoon vessels tied up since December 31st, they're low on fuel and we intercepted and cut off their supply vessel, so I think they're going to be looking at a big loss."

The Steve Irwin was now positioned behind the Nisshin Maru's slipway, blocking them from loading whales, he alleged.

"That can shut down their entire operation," Watson said.

Japan kills hundreds of whales a year under a loophole in the 1986 moratorium on commercial whaling that allows "lethal research", but makes no secret of the fact that the meat ends up on dinner tables.

Anti-whaling nations, led by Australia and New Zealand, and environmental groups have long criticised the hunts, describing them as cruel and unnecessary.