Friends of the Earth and a local pressure group, who brought the action after permission was granted to open the pit in Cumbria last year, said they will contest the ruling.
The groups accuse the government of failing to account for the climate impacts of the coking coal mine, set to open in the town of Whitehaven, on the edge of the Lake District national park.
A ruling by the High Court in London stated that the "application for permission to apply for planning statutory review is refused".
"We still believe that giving the go ahead to the Whitehaven coalmine was unlawful and we will be asking the court to reconsider its decision", said Friends of the Earth campaigner Tony Bosworth.
Senior cabinet minister Michael Gove gave the green light to open the country's first new mine in decades last December, which is meant to be a supposedly "greener" source of coking coal, as it would substitute emissions arising from imports.
The court decision accepted Gove's position based on expert evidence that the plan would have a "broadly neutral effect" with regards to its carbon emissions.
The South Lakes Action on Climate Change (SLACC) argued that the mine would result in a net increase in emissions "at a time when emission reductions are paramount".
It contended that the mine would also undermine the UK's claim to be a global leader on climate change.
The UK has pledged to achieve net-zero carbon emissions by 2050, but the Cumbria mine -- and other plans to allow new North Sea oil and gas exploration -- have angered environmental groups.
"We and our legal team are firmly of the view that there are legal errors in the government's decision to permit the mine," said SLACC chair Carole Wood.
"The government sought to turn a blind eye to the climate impacts from burning the coal that will be produced by the mine, and we look forward to a hearing to consider whether this approach can be lawful."
The government said it would be inappropriate to comment on the case "given ongoing legal proceedings".
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