Police used firearms and tear gas in an attempt to disperse a crowd of several hundred protesters throwing stones near the mine, RIA Novosti reported.
Several dozen demonstrators were arrested.
President Almazbek Atambayev declared a state of emergency in the district, saying the protest "threatens the republic's national security and has significantly damaged the country's economy."
Atambayev said the protest and stoppage of work at the mine could cost the state $125 million and could "cause a serious environmental catastrophe" at the site.
Protesters blocked the road to the Kumtor mine, which is run by Canada's Centerra Gold, and cut electricity to the site earlier this week, RIA Novosti reported.
The protesters are asking for a bigger share in profits from the lucrative gold mine and more investment in local infrastructure from the company.
Kumtor is the largest gold mine in central Asia, producing more than 8.4 million ounces of gold between 1997 and 2011, Centerra's website said.
The Canadian company has denied allegations of causing environmental damage at the mine site,and of tax evasion, RIA Novosti reported.
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