The protesters are demanding that businessman Urmatbek Baryktabasov be allowed to run in the 10 July presidential election.
RFE/RL's correspondent was on the scene and said that the protesters were throwing stones.
Police, firing tear gas into the crowd, forced many of the reportedly unarmed protesters out of the White House and begun chasing them through nearby streets.
RFE/RL's Kyrgyz Service reports there are also protests going on in Karakol, the administration center of the eastern region from which Baryktabasov hails.
Authorities had refused to allow Baryktabasov to register as a candidate, arguing that he had become a Kazakh citizen in the 1990s.
Protesters say the decision is politically motivated as the businessman would pose an electoral challenge for acting President Kurmanbek Bakiev, who is currently visiting northern Kyrgyzstan.
Violence has been increasing as the election approaches. On 13 June, several people were wounded when a crowd of some 200 stormed a hotel in the Kyrgyz city of Osh, in apparent protest against a lawmaker with a financial interest in the business. On 11 June, unidentified assailants burst into Bakiev's campaign headquarters, beating two guards. That incident followed the fatal shooting in Bishkek on 10 June of lawmaker Jyrgalbek Surabaldiev, an ally of ousted President Askar Akaev.
(RFE/RL Kyrgyz Service/agencies)More news and features on Kyrgyzstan