Safety concerns were cited for the decision as the Japanese mother ship, the Nisshin Maru, was obstructed by activists of the Sea Shepherd group, Britain's Guardian reported.
The annual hunting seasons goes on until middle of March but it was not clear if whaling would be halted for the rest of the season.
While commercial whaling has been banned for about 25 years, Japan has relied on a provision allowing hunting for scientific research purposes.
The Guardian said the Nisshin Maru has been chased by Sea Shepherd's Bob Barker vessel ever since the mother ship and the rest of the fleet reached the Antarctic whaling grounds late last year. The mother ship is needed to process the whales caught by the other ships.
The Sydney Morning Herald quoted a spokesman for the International Fund for Animal Welfare's global whales campaign as saying it was hoped the latest development would help show Japan there is no future for whaling in the 21st century.