A Sea Shepherd helicopter spotted the vessel yesterday, 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.
The marine conservation group said the Japanese crew quickly covered the whale with a tarpaulin.
"A soon as the whaling fleet saw 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.
"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.
Photo: Sea Shepherd (Protected Antarctic minke whale on the deck of the factory whaling ship, Nisshin Maru).
Photo Below: Sea Shepherd (The group said the Japanese crew quickly covered the whale with a tarpaulin.