The incident was not believed to be related to activities of Sea Shepherd or any other protest group.
"They have obstructed our activities in the past, and their action is extremely dangerous. They are like pirates"
Japanese foreign ministry
Earlier this week the crew of the Steve Irwin said they had left their pursuit of the Japanese fleet in order to return to port to refuel.
The ship had been pursuing the Japanese whaling fleet for more than 3,000km and have vowed to use all means necessary to prevent the hunt from going ahead.
Japan has said it will ask countries where the Sea Shepherd crew might dock to refuse entry to the vessel.
"We are going to request a port closure against it," Chiharu Tsuruoka, an official with the Japanese foreign ministry, said.
"They have obstructed our activities in the past, and their action is extremely dangerous. They are like pirates."
Last month, the whaling fleet came under attack when Sea Shepherd activists lobbed 25 bottles of foul smelling rotten butter at the fleet.
The group has denied Japanese assertions that the Steve Irwin rammed a Japanese ship.
The Japanese whaling fleet plans to harvest up to 935 minke whales and 50 fin whales this year under International Whaling Commission rules that allow the animals to be killed for research purposes.
But opponents say the Japanese hunt is just a cover for commercial whaling, which was banned in 1986, and that real research into the whales does not necessitate killing them.