Sea Shepherd saboteur actions blamed.
Whalers killed 266 minke whales and one fin whale, well below the approximately 900 they had been aiming for when they left Japan in December.
In the 2010-2011 season, Japan ended the hunt early after killing only 172 whales.
Japan's Antarctic whaling fleet has killed less than a third of the animals it planned to because of sabotage by activists, Tokyo said Friday as it announced the end of the season's hunt.
Japan's Fisheries Agency said the fleet was on its way home from the Antarctic "on schedule", but admitted that at 267 the catch was way down on expectations.
Whalers killed 266 minke whales and one fin whale, the agency said, well below the approximately 900 they had been aiming for when they left Japan in December.
"The catch was smaller than planned due to factors including weather conditions and sabotage acts by activists," an agency official said. "There were definitely sabotage campaigns behind the figure."
Militant environmentalist group Sea Shepherd had pursued the Japanese fleet for much of the season.