"The orders were not made after a hearing. There was no judgment. There were no findings. The orders were made by consent, that is, with the agreement of the parties to the litigation," a spokesman for the court said.

The court spokesman said the "error sufficient to set aside the decision" included the department's own admission the mine would impact the two threatened species – the yakka skink and ornamental snake.

"The Minister found that the proposed action would have a significant impact on two listed threatened species," the spokesman said.

Mr Hunt has refused to blame his own department, saying green groups would "litigate every step of the way, every element of the project through every possible means".

Adani itself accepts that setting aside the federal environment's approval was due to the government's failure.

"It is regrettable that a technical legal error from the federal Environment Department has exposed the approval to an adverse decision," a spokesman for Adani said earlier in the week.

Other legal groups have rejected the government's depiction of the decision.

"Using a term like 'vigilante' when describing a court case – one of the most orthodox and proper methods for challenging government decision making – is extraordinary," Human Rights Law Centre's Senior Lawyer, Ruth Barson​, said.

Mr Abbott has vowed in return to repeal legislation to forbid environmental groups from challenging large developments in court, and only allow those directly impacted by proposals to object.

This has also led to blow back by some legal groups, with the Australian Lawyers Alliance saying the move was "an over-reaction to the Federal Court's Adani ruling".