Fisheries Minister Michihiko Kano said Friday "sabotage" by the Sea Shepherd environmental protest flotilla along with bad weather resulted in the reduced catch of its whaling program, The Australian newspaper reported.
The U.S.-based anti-whaling group follows the Japanese fleet south every year in a bid to disrupt its hunt.
Commercial whaling has been banned for 25 years but Japan catches about 1,000 whales annually in what it says is a scientific research program.
Japan's decision to recall its fleet from the Southern Ocean was welcomed by the Australian government, which said it condemned all commercial whaling, "including Japan's so-called 'scientific' whaling program."
"Japan's whaling activities are contrary to international law," a government statement said. "That is why Australia commenced and will continue legal action in the International Court of Justice."
Anti-whaling groups said they were pleased that the Japanese fleet left the Southern Ocean.
"I think it's been a very successful campaign," Sea Shepard President Paul 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."