The district court decision came just a day after Kyrgyzstan’s parliament passed a law allowing the state to temporarily take over a company if its activities pose a danger to human lives or the environment.
Kumtor, which is owned by Canada’s Centerra Gold, was found by the court to have breached environmental laws by placing waste rock on glaciers.
The company, which has called the charges “entirely meritless”, was fined 261.7 billion som, equivalent to $3.1 billion.
Centerra Gold shares plunged on Friday after parliament passed the company takeover law, as the mining firm warned that the legislation could affect its ownership of the Kumtor mine.
Kyrgyzstan has a long history of disputes with Centerra Gold over how to share profits from the former Soviet republic’s biggest industrial enterprise.
The latest stand-off began shortly after Sadyr Japarov came to power in Bishkek following violent riots last October.
Japarov once campaigned for the nationalisation of the mine and set up a special commission to look into its activities once he became president. $1 = 84.77 Kyrgyz som Reporting by Olga Dzyubenko; Writing by Olzhas Auyezov; Editing by Helen Popper