AP Photo/Sea Shepherd Conservation Society, JoAnne McArthur
Anti-whaling protesters who were trying to stop the creatures being killed have said their high-tech speed boat was attacked in a clash at sea.
The campaigners, who want Japan to stop killing whales for research, accused the whalers of ramming into their boat.
But the whalers said this isn't true, and claimed the protesters threw ropes at their propellers and launched stink bombs at their boat to cause trouble.
The front of the campaigners' boat was ripped off and its side was damaged.
There were six people on board the boat, called the Ady Gil, but they were all rescued.
The anti-whalers, who belong to a group called Sea Shepherd Conservation Society, have been clashing with the Japanese whalers for a few years.
A spokesman for Sea Shepherd said the crash had turned things into a "real whale war".
But the Japanese research team insists it has done nothing wrong and that the protesters have been interfering with their work for years.
The moment the two boats crashed (AP Photo/Institute of Cetacean Research)
Japan used to allow whales to be killed so their meat could be sold for people to eat. This was stopped in 1986, but international laws mean they can still kill some whales for scientists to study.
Some campaigners think this is an excuse and that Japan still kills whales for their meat, but Japan says this is not true.
The protesters are now working to save the Ady Gil and stop it from sinking.