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.
The group hurled stink bombs at the boats and used ropes to try to tangle their propellers in a series of exchanges which saw the whalers retaliate with water cannon.
In the 2010-2011 season, Japan ended the hunt early after killing only 172 whales because of harassment by environmentalists.
Commercial whaling is banned under an international treaty but Japan has since 1987 used a loophole to carry out "lethal research" on the creatures in the name of science.
Japan claims the annual hunt is necessary to substantiate its view that there is a robust whale population in the world. But it makes no secret of the fact that whale meat from the research ends up on dinner tables and in restaurants.
Anti-whaling nations and environmentalist groups routinely label the activity a cover for commercial whaling.
The Australian government welcomed Japan's decision to recall its fleet from the Southern Ocean, saying it condemned all commercial whaling, "including Japan's so called 'scientific' whaling programme".
"Japan's whaling activities are contrary to international law," Canberra said.
"That is why Australia commenced and will continue legal action in the International Court of Justice. Our efforts are aimed at ending Southern Ocean whaling for good."
Sea Shepherd claimed the drastic cut in the harpooners' haul was a victory for them.
"It's been a very successful campaign for us," captain Paul Watson told AFP on Friday. "We chased them for three months, 17,000 miles (27,000 kilometres). They really didn't have much time to catch whales in all that time."
The group vowed to chase the Japanese fleet if it returns to southern waters next season.
"The Japanese were definitely much more aggressive," Watson said from Melbourne, where his ship is now docked. "We had 12 confrontations with the Steve Irwin but no-one was injured on either side.
"They used water cannons, and they threw concussion grenades at us, and bamboo spears and grappling hooks and we hit them back with stink bombs and smoke bombs."