The Indian mining giant's environmental authority has been set aside after the court found Environment Minister Greg Hunt had not properly considered advice about two threatened species – the yakka skink and the ornamental snake.

The Mackay Conservation Group launched its legal challenge in the Federal Court in January, alleging that greenhouse gas emissions from the mine, vulnerable species and Adani's environmental track record had not been taken into account.

"The Minister conceded that he had made an error and Adani did as well that the proper process hadn't been followed in approving the Carmichael mine," Mackay Conservation Group coordinator Ellen Roberts said.

"He is required to take advice from his department on threatened species into account and he didn't do that.

"A lot of new information has emerged since Greg Hunt made his approval and we call on him to now reject the mine."

The project, which will produce up to 60 million tonnes of coal for export a year, has faced fierce environmental opposition because of the proximity of coal terminals at Abbot Point to the Great Barrier Reef.

But it has received praise from both sides of politics, including Prime Minister Tony Abbott, who declared it a poverty-busting miracle for India's poor.

In a statement, the Environment Department said the decision to set aside the approval was a "technicality" and had been done with the consent of all parties involved in the case.

"Reconsidering the decision does not require revisiting the entire approval process," the statement said.

The Environment Department, the minister's office, Queensland's Labor government and Adani are insisting the issue is an administrative matter that will be resolved.

Adani blamed the court's decision on an error by the environment department.

"It is regrettable that a technical legal error from the Federal Environment Department has exposed the approval to an adverse decision," Adani's spokesman said.

"It should be noted the approval did include appropriate conditions to manage the species protection of the yakka skink and ornamental snake.

"However, we have been advised that, because certain documents were not presented by the Department in finalising the approval, it created a technical legal vulnerability that is better to address now."

The department said it had followed "longstanding practice" in providing its advice to Mr Hunt and he had made his decision after "fully considering all of the Department's advice."

"Subsequently the Department has advised that there is a possibility that the advice should have been provided in a particular manner. This is a technical, administrative matter and to remove this doubt, the department has advised that the decision should be reconsidered," the statement said.

The department will now take six to eight weeks to draft new advice for the minister's consideration.

Mr Hunt has not commented on the decision.

The court's ruling is the latest in a series hurdles for the project that have led to questions about whether or not it will proceed.

There are growing calls for the federal and Queensland governments to put a stop to the development and investigate the approvals process for it after information that has been brought to light about Adani's environmental and corporate practices.

Fairfax Media revealed last week that Adani had begun sacking most of its staff at its Brisbane headquarters.

This followed the suspension of Adani's project manager Parsons Brinckerhoff, its construction partner and potential investor Posco, and four engineering firms.

A Fairfax Media investigation in February raised questions about the ultimate ownership of Adani's assets in Australia, as well as the transparency of its corporate structure.

Confidential Queensland Treasury documents revealed in June that treasury officials had also expressed serious concerns to the Queensland government about Adani's transparency and ability to finance the project.

But on Wednesday, Queensland Mines Minister Anthony Lynham continued to praise the project.

"We are extremely disappointed that there has been this delay to Adani in the Galilee Basin,"

"Jobs are so important to the people of Queensland and Adani will bring jobs to a very needed area of Queensland, central Queensland and we look forward to those jobs being produced.

"We are asking the federal government, we are asking the federal environment minister to sort this out as quickly as possible."

- with Amy Remeikis