Japan's whalers ended their season with less than a third of their annual 900-whale quota, catching just 267 whales, BBC News reported.
Japan's Fisheries Agency said the fleet was on its way home from the Antarctic Ocean "on schedule," but blamed activist groups for the small catch, Agence France Presse reported.
"The catch was smaller than planned due to factors including weather conditions and sabotage acts by activists," an agency official told AFP. "There were definitely sabotage campaigns behind the figure."
Activist organization Sea Shepherd proclaimed the victory on their website, writing "Operation Divine Wind is over! The Japanese whalers are going home!"
The US-based anti-whaling group follows the Japanese fleet south every year to disrupt its hunting activities, BBC reported.
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"There are hundreds of whales swimming free in the Southern Ocean Whale Sanctuary that would now be dead if we had not been down there for the last three months. That makes us very happy indeed," Sea Shepherd's president Paul Watson is quoted as saying on the organization's website.
"I think it's been a very successful campaign," Watson told the BBC. "I predicted they wouldn't take over 30 percent and they got 26 percent, so we were right on that one."
Four days before the Japanese left, the Institute of Cetacean Research reported a confrontation between the Japanese ships and Sea Shepherd's ship Bob Barker, CNN reported. The Bob Barker fired over 40 flares and aimed a "high-powered" laser beam at the Japanese ships, according to the institute, which monitors the Japanese whaling industry.
The Australian government applauded Japan's withdrawal of its' whalers.
"Japan's whaling activities are contrary to international law," the government said, according to the BBC. "That is why Australia commenced and will continue legal action in the International Court of Justice."
Despite a worldwide ban on whaling, Japan conducts "legal research" on whales each year through a loophole which allows whale-hunting for scientific purposes, BBC reported. However, activists claim the research is just a cover for commercial whaling.