The Interior Ministry ordered troops to surround the government building where protesters gathered and later armed police appeared also.
Kyrgyz President Kurmanbek Bakiev eventually came out to meet with protesters and called on them to disperse peacefully.
"I believe that the justice system will make a decision in the framework of justice and law, that is why I ask you, I appeal to you, who have gathered here today, please do not disturb [public] order in the city, and disperse peacefully and safely," he said. "The court should make its own decision."
Most of the protesters came from the northeastern Issyk-Kul region, where Akmatbaev hoped to be a candidate.
Akmatbaev said he would appeal the commission's decision. A court is expected to hear that appeal next week.
ONE YEAR AGO: Click on the image to view RFE/RL's archive of coverage of Kyrgyzstan's Tulip Revolution from the beginning, including biographical sketches of the key players and photo galleries of the demonstrations.
See RFE/RL's special review of the March 2005 Kyrgyz events:
THE COMPLETE KYRGYZSTAN: To view an archive of all of RFE/RL's coverage of Kyrgyzstan, click here.