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.
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.
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.
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.