The Institute of Cetacean Research, which organises Japan’s so-called scientific whaling program, says activists from the Sea Shepherd conservation group have confronted the fleet in the Southern Ocean.
It has accused the anti-whaling campaigners of throwing glass bottles at its harpoon ship.
It says activists on board Sea Shepherd’s speedboat also threw ropes at the whaling ship’s propeller.
No-one was hurt in the clash.
The Japanese fleet is in Antarctic waters harpooning whales for what it says is scientific research.
Opponents of the hunt say it is a cover for commercial harvesting.
The clash follows an earlier attack by the Sea Shepherd’s other ships Steve Irwin and Bob Barker against the Japanese whaling ship Yushin Maru 3 in Antarctic waters on New Year’s Day.