The project to build a huge open-cast mine and port near the National Humboldt Penguin Reserve had been shut down in August 2017 by a ministerial panel over the risk it posed to the local environment.
Andes Iron, a Chilean company, wanted to extract millions of tonnes of iron in Coquimbo, a region about 450 kilometres (280 miles) north of Santiago.
But the area comprises a nature reserve encompassing three islands which are home to 80 per cent of the world's Humboldt penguins as well as whales, sea lions and otters.
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Following the ruling, Andes Iron appealed, filing a claim which on Friday was accepted by a court in the northern port city of Antofagasta.
In its decision, the court annulled the ministerial decision and ordered that a new assessment be made on its environmental impact to decide whether it can go ahead or not.
Should it be approved, the $2.5 billion project would involve the extraction of 12 million tonnes (tons) of iron ore a year along with 150,000 tonnes of copper, making it the biggest such venture in Chile.
It would also involve the construction of a port, with the sprawling project sparking a bitter national debate over economic development versus environmental conservation.
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Environmentalists have vigorously opposed the plans, saying it would sound the death knell for an area of Chile rich in natural resources which is known for its environmental diversity.
Following Friday's ruling, conservation group Oceana said it would appeal to the Supreme Court, warning that the project would endanger "one of the world's most important marine ecosystems, which has been recognized by national and international scientists as a hotspot of biodiversity which must be protected."
Oceana has said the mine and the increased shipping traffic it would generate would do untold harm to a known cetacean migrant route whose pristine waters provide a rich food source to several vulnerable species.
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