The fleet caught only 551 minke whales, compared with the planned catch of 850. No fin whales were caught at all, although it had set a target of 50, a Fisheries Ministry official said.
"Sabotage by activists is a major factor behind our failure to achieve our target," the official said.
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.
The absence of fin whales in the catch was partly due to other factors, the ministry said.
"Sabotage is not entirely to blame for that. There was a situation where few fin whales were spotted," the official said.
Greenpeace Japan, which also carried out activities aimed at obstructing the hunt, said it was not satisfied with the reduced catch.
"They say that one reason for the lower catch is that they didn't see so many whales," said Junichi Sato of Greenpeace. "That is a good reason why they should not conduct lethal research."
He added that, despite the reduction, the number of whales actually killed was more than three years ago.
International criticism forced Japan to give up a plan to catch 50 humpback whales, a favorite with whale watchers.
The clashes sparked a spate of diplomatic complaints between Japan and Australia.
The Australian government has promised to try to stop Japan's whaling program and is considering international legal action, although the two countries have agreed not to let the issue hurt ties.
Japan's coastguard 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 program the following year.
Japan's whaling fleet has killed about 7,000 Antarctic minkes over the past 20 years.
© 2008 Reuters