The whalers, who were chased for much of their hunt by activists' boats, were to return starting Tuesday with 551 minke whales, far less than the original plan to kill up to 935 minke and 50 fin whales.
Japanese whalers hunt under an internationally permitted research program, despite a 1986 ban on commercial whaling. Critics say the research program is just commercial whaling in disguise, and demand it be stopped.
"We did not have enough time for research because we had to avoid sabotage," Japan's Fisheries Agency said in a statement Monday, referring to the protesters.
The fleet last year had also planned to kill 50 humpbacks in the Antarctic for the first time in decades, but was forced to abandon that in December in the face of protests by the United States and other governments.
Anti-whaling activists - notably from the group Sea Shepherd - clashed with the Japanese fleet throughout the season, blocking their path and pelting boats with containers of rancid butter and acid, slightly injuring several crew members. In January, two Sea Shepherd activists jumped onto one of the Japanese ships and spent several days in detention on board.
Japanese officials also said the fleet spotted fewer minke whales than they had in the same area two years ago.
Officials, however, stopped short of concluding there were fewer whales.
"We have to wait for a scientific analysis to determine whether the number is in decline or not," said Shigeki Takaya, a Fisheries Agency official in charge of whaling.
Activists cheered the results of their efforts to block the hunt. But Junichi Sato, whaling project leader for the environmental group Greenpeace, said even the reduced hunt killed too many whales.
"It is still above the 400 or so they caught about three years ago. So it's a lot compared with several years ago," he said.
Japan's hunt, which provides supermarkets and upscale restaurants with whale meat, has come under increasing international pressure in recent years as Tokyo has expanded its catch.
Japan has failed in efforts to have the International Whaling Commission strike down the commercial whaling ban and grant wider hunting rights to small-scale coastal whalers, and has threatened to resign from the commission.
Tokyo has long argued that the whaling ban should only apply to endangered species. It also accuses the West of hypocrisy for criticizing current Japanese whaling after American and European whalers nearly wiped out the mammals in the 19th and 20th centuries.
The Japanese have hunted whales for centuries, and whale meat was widely eaten in the lean years after World War II. The meat, however, has plunged in popularity in today's prosperous Japan, and is only eaten regularly in small coastal whaling communities.
