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The conservation group located the Japanese fleet on Friday night, and two of its vessels were now ahead and behind the factory ship Nisshin Maru.
Sea Shepherd New Zealand spokesman Michael Lawry said the Japanese fleet, including its harpoon and security vessels, was now leaving the whaling grounds.
"They were heading northeast, out of the area, and the Sea Shepherd vessel Bob Barker was right on the tail of the factory ship, and the Steve Irwin was ahead."
Mr Lawry said the group's presence had put a stop to Japan's whaling.
"If they're moving, they're not whaling, and if we're on the tail of the factory ship, they won't be whaling.
"The plan will be just to stay on their tail and drive them out, pretty much. If we can stay on their tail, then they won't be able to load any more whales on."
The Steve Irwin's helicopter spotted the Nisshin Maru and its two harpoon ships on Friday night, after heavy fog lifted. Sea Shepherd's vessels quickly made their way towards the Japanese fleet.
The anti-whaling group said it was able to find the fleet thanks to information from Australian Environment Minister Greg Hunt.
It was also able to track the fleet by the discarded, bloody remnants of dead whales, which Sea Shepherd said had been strewn through the water of the Southern Ocean.