A Kyrgyz Health Ministry official said at least 55 people were injured in the clashes in the village of Barskoon, including 13 police officers.
Authorities responded by declaring a curfew and state of emergency, effective until June 10.
RFE/RL's correspondent reports from the scene that police used tear gas against the crowd and that concussion and fragmentation grenades exploded near the scene where around 3,000 protesters were gathered.
The clashes erupted after police arrested dozens of protesters who had seized an electricity station and cut off power to the Kumtor gold mine late on May 30.
The protesters reportedly took a local governor hostage but later released him.
Kyrgyz President Almazbek Atambaev announced the state of emergency for the entire Jety-Oguz district in which the Kumtor mining operations lie. It includes a curfew between the hours of 9 p.m. and 6 a.m.
The main road near Kumtor remained blocked by hundreds more protesters early on May 31, with local authorities trying to negotiate with them.
The protesters at one point were demanding a meeting with Kyrgyz President Almazbek Atanbaev and Prime Minister Jantoro Satybaldiev.
The Kumtor mine, which accounts for 12 percent of the Kyrgyz economy, has been at the center of political turmoil for several months now.
Local groups have been demanding that Centerra Gold build environmentally friendly infrastructure and medical facilities for them.
In October, some 1,000 demonstrators demanded the nationalization of Kumtor in a violent protest in the capital, Bishkek.
Three opposition lawmakers who took part in the October protest have been found guilty of attempting to seize power by force and sentenced to prison terms between a year and 18 months in March.
On May 31, hundreds of protesters in the southern city of Jalal-Abad demanded the immediate release of the three lawmakers.
They occupied the offices of the regional governor and announced that they have elected their own "people's" regional governor, Medet Usenov, who led the May 31 rallies.
Earlier this month, a Kyrgyz government commission started looking into potential environmental problems that could be caused by unstable waste heaps at Kumtor after opposition parties raised concerns.
In February, also after requests by opposition parties, the Kyrgyz parliament gave the government three months to renegotiate the terms of the 2009 contract on Kumtor.
The deal granted Centerra Gold a low tax rate that officials now say deprives Kyrgyzstan's budget of many millions of dollars.
In a statement on May 30, Centerra Gold warned its gold production and "financial results" would be negatively affected if road access was not restored soon.
Kyrgyz Prime Minister Satybaldiev told journalists on May 31 that his government plans to force the organizers of the protest to pay for all the losses caused by the situation.