It's the latest blow for the miner in the Central Asian nation, coming a day after the government passed a new law allowing it to take interim control of KGC and its bank accounts if it posed a threat to people's lives or health.
The district court decision to fine the company 261.7 billion som was reported by wire services on the weekend.
Centerra had last week flagged the new threat of $3 billion being sought in damages, for its past practice of storing waste rock on glaciers, but said its 2019 strategic agreement with the government had released the company and KGC from all outstanding claims at the time.
It is also facing a $170 million tax bill and is aware of other draft laws and decrees brewing to undermine its 2009 restated Kumtor project agreements.
It believed all claims were "entirely meritless" but had warned on Friday there were no assurances disputes could be resolved without a material impact on the company.
Kyrgyz's new president Sadyr Japarov, who earlier fought to nationalise Kumtor, took office in January following post-election chaos and has formed a special commission to review Kumtor's activities.
Centerra describes Kumtor as the largest private sector employer and taxpayer and the largest foreign investment in the country.
The mine produced 556,136 ounces of Centerra's 2020 output of 824,059oz, with the remainder coming from its Mount Milligan in British Columbia and Oksut in Turkey.
Centerra is due to release its March quarter results later today.
Its shares reached a new one-year low of C$8.21 intraday and closed down 1.7% yesterday to $8.25, valuing it about $2.4 billion (US$2 billion).