Repeated "sabotage" by activists forced Japan's whaling fleet to catch only 551 whales in the Antarctic, far short of its target under what it calls an annual research whaling programme, the Fisheries Agency said on Monday.
Japan had planned to catch about 850 minke whales in the Antarctic during the hunting season.
"We caught 551 minke whales, far below our original target," said a Fisheries Agency official.
"Sabotage by activists is a major factor behind our failure to achieve our target."
Militant anti-whaling campaigners from the Sea Shepherd Conservation Society had repeatedly confronted Japan's whaling fleet earlier this year.
Last month, members of the Sea Shepherd group threw bottles and containers of foul-smelling substances at a whaling ship in an attempt to disrupt the hunt, resulting in three sailors complaining of eye irritation.
The incident followed a high-profile standoff in January in which two activists boarded another Japanese whaling ship, forcing it to suspend whaling for a month.
Japan also planned to hunt 50 fin whales, but the fleet failed to catch any due partly because of confrontations with the anti-whaling campaigners, the official said.
"Sabotage is not entirely to blame for that. There was a situation where few fin whales were spotted."
International criticism forced Japan to give up a plan to catch 50 humpback whales under the program.
The clashes sparked a spate of diplomatic complaints between Japan and Australia.
The Australian government has promised to try to stop Japan's whaling programme and is considering international legal action, although the two countries have agreed not to let the issue hurt ties.
Japanese coast guard and police will inspect the country's whaling fleet this week after the clashes with the conservation activists, local media reported on Sunday.
The six-ship fleet is expected to return home on Tuesday.
Japan, which considers whaling a cultural tradition, abandoned commercial whaling after agreeing to an international whaling moratorium in 1986. But arguing that the hunt is necessary to study whales, Japan began what it calls a scientific research whaling programme the following year.
Japan's whaling fleet has killed about 7,000 Antarctic minkes over the past 20 years. (Reporting by Teruaki Ueno; Editing by David Fogarty)