Australian Prime Minister Julia Gillard has warned anti-whaling activists in the Southern Ocean not to take dangerous risks.
Japan's Institute of Cetacean Research has called on Australia to take criminal action against the Sea Shepherd Conservation Society after a confrontation on Sunday.
The Sea Shepherd fleet harassed the Japanese whalers in a bid to prevent any whales being killed, and were hosed with high-pressure water cannon.
Ms Gillard says the federal government doesn't want to see anybody come to harm at sea.
"My primary message to the crew of the Sea Shepherd, and to any other vessel in the area, is that they need to conduct themselves appropriately so everybody is kept safe," she says.
"The important thing is to make sure everybody is kept safe in what is a remote, dangerous and very inhospitable part of the world."
The latest confrontation has led the Greens and the Federal Opposition to call for greater surveillance of whaling in the Southern Ocean.
The Opposition wants the Government to send a Customs ship to the area but Greens leader Bob Brown says the Navy should be used instead.
"It's high time the Australian Government sent either aerial surveillance or naval presence down there to video the slaughter and send it to the rest of the world," he says.