Supporters of Almazbek Atambayev threw rocks, turned over and set fire to garbage cans, while police used tear gas and stun grenades to disperse the crowds.
The violence has raised the threat of a new round of turmoil in the ex-Soviet nation, which borders China and hosts a Russian military air base.
Kyrgyzstan’s first two presidents after independence were both driven from office by riots.
Almazbek Atambayev, who was in office from 2011 to 2017, accused his successor and protégé, current President Sooronbai Jeenbekov, of fabricating false criminal charges against him to stifle criticism.
He urged his supporters to rally Thursday in the capital, Bishkek, to demand Jeenbekov’s resignation.
The first attempt by police to arrest Atambayev at his residence outside the capital failed late Wednesday after his supporters rushed to his defense and clashed with police.
A police officer later died of his injuries at a hospital and 79 people were injured, according to official statements.
Atambayev’s supporters took six policemen as hostages, but released them Thursday.
Police returned in bigger numbers and used water cannons and stun grenades to overwhelm Atambayev’s supporters.
Atambayev was driven to the headquarters of the State National Security Committee in the capital.
About 1,000 Atambayev supporters later arrived in Bishkek and tried to rally outside the presidential office, but police quickly dispersed them with tear gas and stun grenades.
Police also tightened controls on the city’s fringes and clashed with other pro-Atambayev supporters who were trying to drive into the capital.