The case was centred on whether federal Environment Minister Tanya Plibersek was legally required to scrutinise climate change impacts associated with new coal and gas projects.
The Environment Council of Central Queensland lost the first round last year, when Federal Court judge Justice Shaun McElwaine dismissed the case.
The council appealed, but on Thursday the full bench of the Federal Court also dismissed the matter.
Environmental Justice Australia, representing the council, hoped a win could change the way dozens of coal projects on the minister's desk are assessed.
AAP is seeking comment from the council about Thursday's loss.
In last year's ruling, Justice McElwaine said the minister did not dispute that many aspects of the environment had been or would be affected by climate change.
Nor did Ms Plibersek dispute that emissions from the burning of fossil fuels had contributed to global warming.
In a previous ruling, Tanya Plibersek didn't dispute that fossil fuels had contributed to warming. (Mick Tsikas/AAP PHOTOS)
But despite her acceptance of those things, Justice McElwaine said existing laws did not oblige her to do anything differently when considering fossil fuel projects.
The case was centred on plans to expand two NSW coal mines at Narrabri and Mount Pleasant.
The companies behind the projects - Whitehaven Coal subsidiary Narrabri Coal Operations, and MACH Energy - joined the proceedings in support of the minister.