A Japanese harpoon strikes the whale with a stomach-turning thud. The exhausted animal is hauled from the water, flesh torn, purple organs spilling from its body.

This is the shocking evidence of a Japanese whaling hunt in an Australian whale sanctuary that the federal government did not want you to see.

After a five-year freedom-of-information battle, marine conservation group Sea Shepherd has obtained unreleased footage, shot by Australian customs officials, which reveals in distressing detail the killing of a minke whale by a so-called Japanese "research" ship.

The federal government fought to have the footage kept secret, arguing that it would harm relations with Japan – prompting accusations it prioritised diplomatic interests over protecting the whales and representing the views of Australians who want the annual killing spree stopped.