Over 50 people were wounded and 80 detained in the clashes, authorities said.
The protest also triggered widespread unrest in the southern city of Jalal-Abad, where hundreds stormed the governor's office.
The twin developments threatened further turmoil in this impoverished Central Asian nation of five million, which hosts a U.S. base supporting military operations in nearby Afghanistan.
Protesters want the northeastern Kumtor gold mine to be nationalized and the company to provide more benefits.
The mine, operated by Toronto-based Centerra Gold (TSX:CG), is the largest foreign-owned gold mine in the former Soviet Union. It accounts for about 12 per cent of the nation's economy and has been at the centre of heated debate between those favouring nationalization and officials who believe that would deter much-needed foreign investment.
Centerra said Friday that an orderly shutdown of its milling facility using power from a backup diesel generator was continuing and that mining operations have been suspended other than those to manage ice and waste.
"Until safe and secure access and grid power has been restored to the facility it will not be possible for the company to determine the extent of the impact on the operations, including gold production and financial results," the company said in a statement.
Shares in the company closed down 33 cents or nearly eight per cent at $3.82 on the Toronto Stock Exchange on Friday.
The demonstrations began earlier this week when protesters blocked the road leading to the mine in the northern Tian Shan mountains.
On Thursday night, several hundred demonstrators, some on horseback, besieged a power transformer unit in the village of Tamga and cut off electricity to the mine for several hours. Riot police moved in overnight, detaining about 80 protesters and restoring the power supply.
By Friday, riot police used stun grenades and rubber bullets to disperse some 2,000 protesters who attempted to storm the Kumtor mine office, the Health Ministry said.
It said at least 55 people, including 13 police, were wounded in clashes and a police bus was set on fire.
Kyrgyz President Almazbek Atambayev declared a state of emergency in the area and the Defence Ministry announced it was deploying forces to protect key facilities.
A senior cabinet member visited the area Friday and tried to persuade the protesters to disperse, saying that further disruptions would cripple the mine and cause significant economic losses.
"The government is asking you to have patience and wait until the autumn, when we will look at the issue," Deputy Prime Minister Shamil Atakhanov told protesters.
But shortly after he spoke, protesters went back to the power transformer unit and cut the power again, forcing the mine to suspend operations.
The protest quickly spread, engulfing the southern city of Jalal-Abad, where several hundred people stormed a local governor's building, drove officials out and appointed one a "people's governor," the Interfax news agency reported.
The man, Medet Usenov, told Interfax the protesters were demanding the release of several opposition lawmakers jailed on coup attempt charges last October when a demonstration in the capital of Bishkek to demand the nationalization of Kumtor spiralled into a violent confrontation with police.
He added that they intend to name local mayors and district administrators throughout Jalal-Abad province.
Kyrgyz media speculated on Friday that the current government's political rivals could be behind the protests. Former Kyrgyz President Roza Otunbayeva told the AKIpress news agency that they are a planned attempt to topple the government.
Politics in Kyrgyzstan are shaped by clan loyalties and sharp divisions between the north and the south. The ex-Soviet nation on China's mountainous western frontier has seen the violent overthrow of two governments since gaining independence in 1991.
In 2010, the government was overthrown and clashes between ethnic Kyrgyz and minority Uzbeks killed at least 470 people, mostly Uzbeks, and displaced about 400,000 people.
Vladimir Isachenkov contributed to this report from Moscow.Suggest a correction