"The Southern Ocean is a dangerous and inhospitable part of the world," said a statement from Peter Garrett, Australia's environment minister.
No one was injured in Saturday's collision, in which each side blamed the other, The Sydney Morning Herald reported.
The Sea Shepherd ship Bob Barker suffered a yard-long gash in the collision with the Yushin Maru 3 in their first meeting since the sinking of the 16-ton Ady Gill in a collision with the whaling fleet's security ship, Shonan Maru 2.
Despite the damage, the Bob Barker remained in pursuit of the Yushin Maru 3 as it headed toward the coast of the Australian Antarctic Territory, Paul Watson, the head of Sea Shepherd, said Saturday night.
Watson said the whalers were using water cannons and acoustic devices against the crew of the Bob Barker while Japanese officials accused the Sea Shepherd crew of trying to blind them with a high-powered laser device.