The mega project in Queensland's Galilee Basin, which would become Australia's largest coal mine, was challenged by Conservation group Coast and Country in Brisbane Land Court on the ground that it would affect groundwater, climate change and biodiversity, including black-throated finches, an endangered species.
Conservationists fear that the project threatens the fragile Great Barrier Reef and vulnerable species while worsening global climate change.
"Those conditions include six hour monitoring of water bodies from dawn and greater assessments and surveys of the black-throated finch," it said.
MacDonald also ordered that the Ten Mile Bore region be investigated to determine their importance in sustaining the black-throated finch population.
The court's decision is a win for the Indian firm, which has been battling legal challenges and recently asked Prime Minister Malcolm Turnbull to create special laws to block objections from green groups, the Brisbane Times reported.
Adani claims its project will deliver 10,000 direct and indirect jobs, and 22 billion dollars in taxes and royalties.
Adani's own witness Jerome Fahrer told the court this year the project would create an average of just 1,464 jobs annually, an assessment MacDonald agreed with.
"Fahrer's evidence, which I have accepted, was that the Carmichael Coal and Rail Project will increase average annual employment by 1206 fte [full time equivalent] jobs in Queensland and 1,464 fte jobs in Australia," she ruled.
But she said this was not enough to lead her to conclude the project should not go ahead. "Rather, I shall draw this information to the attention of the Minister," she said.
Adani welcomed the decision as one that "recognises the pivotal role the resources sector plays in Queensland, subject to strict regulations".
(Reopens FGN 11)
"This significant decision recognises the thorough, science and evidence-based work Adani and its partners have undertaken over more than five years to demonstrate the company's commitment to complying with both Queensland and Australia's world's best practice environmental protections," the Adani spokesman said.
"Today's decision will pave the way to the destruction of some of Queensland's most beautiful ecosystems," he said.
"Days after a binding international climate agreement here we see an Indian mining company seeking to develop a massive coal mine," he said, referring to Paris climate deal which is intended to curb the use of fossil fuels.
The Queensland Resources Council chief executive Michael Roche said the decision showed the environmentalist group's claims were unfounded.
"This judgement is a comprehensive rejection of the activist argument against this huge job generating project, it's rejected the activist arguments around the financial viability of the project, it's rejected the activists arguments around the issue of climate change," he said.
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