The protesters on Friday tore down cast-iron railing surrounding the building, where the electoral commission is housed, and rushed in, sweeping aside some 50 policemen and 20 national guardsman who had been patrolling the building.
Some reports put the number of protesters at several hundred and said 500 policeman stood by as they entered the building.
Shortly after the storming, some 1000 anti-riot police arrived at the site and surrounded the protesters.
The crowd had earlier gathered outside the building, shouting slogans in support of the candidate, Urmat Baryktabasov, before forcing their way in.
The electoral commission on Monday rejected Baryktabasov's candidacy, stating that he had accepted citizenship from neighbouring Kazakh three years earlier and was no longer Kyrgyz.
The issue was due to be taken before the Bishkek court on Friday.
The electoral commission announced that seven candidates had been officially registered to take part in the 10 July presidential poll, including frontrunner and interim President Kurmanbek Bakiyev, former interior minister Keneshbek Duishebayev and former education minister Gaisha Ibragimova.
The election was called after a March uprising ousted longtime Kyrgyz president Askar Akayev.