The incident happened about 300 miles north of Mawson Peninsula off the coast of Antarctica.
Anti-whaling group Sea Shepherd said whaling crew used grappling hooks and a bamboo pole to strike the activists.
Japan's Institute of Cetacean Research said the activists had tried to cut ropes and tangle the Japanese ship's propellers with ropes.
Sea Shepherd follows the Japanese fleet south every year in a bid to disrupt its hunt.'Sabotage'
A statement on the Sea Shepherd website said the Japanese crew of the Yushin Maru No 2 threw grappling hooks at the activists, who were in two small boats.
They were attempting to slow the Japanese harpoon vessel, which was on the tail of the group's ship, the Steve Irwin.
A statement on the website of the Institute of Cetacean Research (ICR), which sponsors Japan's whaling activities, said the activists were trying to ''sabotage'' the Yushin Maru, throwing ropes with hooks attached and also hurling glass bottles of paint.
"When the activists started using a knife to cut the YS2 float fender rope and net, the Japanese vessel crew used bamboo poles as a measure to push the boat back," said the statement.
The Japanese have also released a video of the incident showing a water canon on the Yushin Maru being sprayed at a rubber dingy while objects were being thrown at the ship by the activists.
Japan's fleet sails south to the Antarctic in the autumn each year, returning the following spring.
There has been a ban on commercial whaling for 25 years, but Japan catches about 1,000 whales each year in what it says is a scientific research programme.
Critics say it is commercial whaling in another guise.
In the past there have been clashes between activists and whalers, and collisions between Sea Shepherd's vessels and the whaling fleet.
Last week, Japan handed three anti-whaling activists who had boarded a whaling support ship back to Australian authorities.