Species likely to be affected by the project included the endangered Abbott’s booby, whose rainforest home on the island is the last remaining nesting habitat for this bird in the world, and the endangered cave fern, the minister said in his statement.

Fairfax Media sought comment from Phosphate Resources.

The project failed an assessment under the Environment Protection and Biodiversity Conservation (EPBC) Act, joining only 10 other proposals blocked since the law came into effect in 1999.

Along with the threat to habitat, the project also posed "a very real threat" of introducing aggressive weed species, the government said.

Christmas Island - a 135 square-kilometre Australian territory, about two-thirds of which is protected in a national park - is famous for its annual mass migration of millions of red crabs.

It has also had its environmental setbacks, such as the Christmas Island pipistrelle, a tiny bat species found only on the island that was formally declared extinct last year by the International Union of Conservation of Nature. It was last seen in 2009.