A year after opening there was an accident when a delivery truck carrying over 1700 kg of cyanide fell into the Barskaun river valley below, which flows into Lake Issyk-Kul. There were several fatalities due to poisoning from the spill and up to 2500 people fell ill. After long protests and political struggle, 4 million USD was paid in compensation.

More recently the mine has been in the news when there were protests and road blockades by local groups who fear that the mine is an ecological time bomb and blame pollution from the mine on birth defects in both human and animal populations, including reports of dwindling fish stocks. There are fears that the toxic tailing ponds could be affected by the increase in glacial meltwater that is occurring annually and this could eventually lead to a catastrophic overspill into the rivers and lake below.

A woman leader of the local opposition to the mine, Erinkgul Imankojoeva, said that an outburst of the Petrov's glacier can cause environmental disaster not only for Kyrgyzstan, but for Central Asia. The Petrov's glacier, which 23 km in length, melts for 61 meters per year which leads to increase of the Petrov's lake in size. The tailing storage facility of Kumtor is 1 km beneath the dam of the lake."If the lake outbursts for the entire depth of the dam, then the tailing storage facility would be washed out.”

The Kyrgyz government wanted to renegotiate their interest in the mine (about 33%). Centerra's tax payments to the government, currently accounts for 12% of GDP for the country. During the protests in 2013 thousands of protesters blocked roads and disrupted power supplies to the massive open-pit mine, demanding better ecological standards and free medical facilities. The government ultimately sent in troops to quell the protests and remove the blockades that had been built. The government has been using the claims of environmental damage to call for an increased share in the wealth generated by the mine. There are no agreements for financial assurance in the case of environmental damage after the mine has closed.

The company clearly believes that the profits from the mine (and the resulting taxes) are important for itself and the country and clearly the Kyrgyzstan government views the revenue as vital. So despite the government's attempts to get a larger share of the mine based on environmental risks posed by production and waste, they would still no doubt maintain production at the mine due to its economic importance. The locals only received compensation after lengthy legal battles with the mine.

With regard to social metabolism, Kronenberg (2013) recently highlighted the case of Kumtor mine and its impact on glaciers in the area it operates. By the end of 2011 39 million metres cubed of ice had been removed at the site. In light of the growing recognition of the vital role that glaciers play in ecosystem, especially with regard to global warming, Kronenberg compares a mine in South America with Kumtor mine, both involved in the removal of glacier cover, and concludes by noting the importance of democratisation and social empowerment for environmental governance. Kyrgyzstan's political traditions and social legacy of long-term top-down rule (especially as a former republic of the Soviet Union) make civil society contestation difficult.

In February 2014 it is reported that Centerra Gold and the Kyrgyz Republic have made peace, as the country’s Parliament approved the creation of a joint venture that evenly splits control of the Kumtor gold mine with its Canadian owner. The deal increases Kyrgyzstan's 32.7% equity interest in Centerra to a 50% stake in a joint venture that would own and operate the mine. Among other things, the resolution by the Parliament calls for further audits of the Kumtor operation and for the Government and the General Prosecutor’s Office to continue pursuing claims for environmental and economic damages, which Centerra disputes.

In April 2014 a new glacier law could affect Kumtor mine, which is bisected by a glacier.

The ‘glacier law’ must first be signed by the Kyrgyz President before it would take effect. The new law contains provisions for paying compensation for damages to glaciers, at rates to be determined by the government.

Centerra believed that any disagreement regarding the application of the glacier law to Kumtor should be subject to the dispute resolution (international arbitration) provisions of the Kumtor project agreements.