Sea Shepherd says it has caught Japanese whalers in Australian waters with a slaughtered whale on board.

The group has released pictures showing a dead protected minke whale on board the Japanese whaling ship Nisshin Maru, allegedly in Australian waters.

A Sea Shepherd helicopter spotted the vessel on Sunday morning with two harpoon ships nearby.

"They're hit with an explosive harpoon that goes straight into their body, hooks come out and shrapnel is sent through their body, it's a terrible bloody death… these whales can take up to 30 or 40 minutes to die," Jeff Hansen from Sea Shepherd said.

Sea Shepherd claims the Nisshin Maru was in Australian waters. ( Supplied: Sea Shepherd )

The group says the Japanese crew quickly covered the whale with a tarpaulin.

"A soon as the whaling fleet saw that Sea Shepherd on the scene, they were scrambling to cover up their illegal operations, they were covering up their harpoons," Mr Hansen said.

"This is all happening deep in Australia's whale sanctuary off the Antarctic coast.

Sea Shepherd's Jeff Hansen said the images and video have been handed to the Australian Government. ( ABC News: Courtney Bembridge )

"It shows that even with the Japan Prime Minister on Australian soil, Japan is going about their bloody business ignoring the Australian Federal Court ruling, ignoring the wishes of the International Court of Justice."

Sea Shepherd said it had handed its vision to the Federal Government and urged it to take immediate action.

"Once again there's blood in the water, in Australian waters, and there's a blind eye in Canberra," Mr Hansen said.