Environmental group Sea Shepherd Conservation Society says its harassment of whalers in the Southern Ocean has resulted in another unprofitable season for the Japanese.
Japan has confirmed the fleet decided to return home on Tuesday earlier than planned after catching less than a third of its quota in the Antarctic this summer.
A New Zealand-based spokesperson for Japan's Institute of Cetacean Research says 266 minke whales out of a quota of 935 and just one fin whale out of a quota of 50 were caught.
He told Radio New Zealand News on Saturday the take was low because two of the fleet's six ships had to stop whaling and monitor the whereabouts of Sea Shepherd vessels.
The spokesperson says the total will be satisfactory to the Japanese government which funds the expeditions.
Sea Shepherd president Paul Watson says his group would have been even more effective if one of its boats, the Brigitte Bardot, had not been damaged by a wave.
He says he is already thinking about next season.
"If they return next year we will return stronger than ever. We plan to bring back four ships, two helicopters and 120 volunteers with two scout ships."
Mr Watson, told Radio New Zealand News the fleet needed to catch 550 whales to break even.
"It was quite successful - not as successful as last year, but certainly far more successful than the previous years. But overall, we chased them for 17,000 miles, kept two of their harpoon vessels out of the whaling game for the entire time.
Mr Watson estimates the Japanese expedition would have lost almost $NZ50 million this season.
A ban on commercial whaling has existed for 25 years, but Japan catches about 1000 whales each year in what it says is a scientific research programme.