Police officers protecting the government building, known as the White House, used dogs and smoke bombs to disperse a group of young men who attempted to scale the gates.
Around 1,000 people gathered in the centre of the city for a rally, organized by nationalist politicians Sapar Zhaparov and Kamchibek Tashiyev, ostensibly to demand the nationalization of the Kumtor gold mine, owned by a Canadian company.
Kyrgyzstan, a country of five million people on China's mountainous western border, has come to prominence in recent years because it hosts a U.S. airbase used to support military operations in nearby Afghanistan.
Kyrgyzstan is currently governed by a broad parliamentary coalition presided over by Prime Minister Zhantoro Satybaldiyev. Zhaparov and Tashiyev are members of a virulently nationalist opposition party, Ata-Zhurt, which draws the bulk of its support from the south of the country, which was the scene of deadly ethnic clashes in June 2010.
The politicians have in recent months come out in increasingly vocal opposition to the government.
Wednesday's gathering was intended to voice discontent over the mine, which has been the source of a series of toxic spills in past years.
Critics have alleged that Toronto-based Centerra Gold (TSX:CG), which is developing Kumtor, has used accounting tricks to reduce its tax liabilities. The company has denied the allegation.
Centerra says its project has generated $1.9 billion in benefits for Kyrgyzstan, including $620 million in taxes. Kumtor accounts for 12 per cent of the economy