The fire aboard the Nisshin Maru two weeks ago killed one crew member and left the vessel unable to sail under its own power for 10 days, prompting strong protests from the New Zealand government and from the environmental group Greenpeace over potential oil and chemical spills or damage to penguin colonies.
"This is the first time in 20 years that we've had to cancel our research," said Takahide Naruko, the head of the Fisheries Agency's Far Seas Division. "We are very disappointed."
The fleet had been originally scheduled to continue its hunt through the end of March and return to Japan in mid-April. It had a target catch of 860 whales, Naruko said, and they killed 508.
The fleet is part of a whaling program that Japan claims provides crucial scientific data for the International Whaling Commission — which sanctions the annual hunts — on populations, feeding habits and distribution of the mammals in the seas near Antarctica.
The program has long been the target of environmental groups, which claim it is a pretext for Japan to keep its whalers afloat despite an international ban on commercial whaling in effect since the 1980s. After researchers complete their studies of the killed whales, the meat is sold in Japan for food.
Greenpeace and other environmental groups claim sufficient research could be done without killing the whales.
The accident has been a major embarrassment for Japan, one of the main proponents of lifting the commercial whaling ban.
New Zealand Prime Minister Helen Clark said Monday the Nisshin Maru — carrying 343,000 gallons of fuel oil — posed a huge risk to the pristine Antarctic environment and called it a "disaster."
A Greenpeace vessel, in the area to protest the hunts, offered to tow the ship into calmer seas. The whalers declined the offer.
Japanese officials stress that no oil has leaked from the ship and said it has safely moved away from the Antarctic coast under its own power last weekend after floundering near the world's biggest Adelie penguin rookery.