At Prison No 31, 25 km (15 miles) from the capital Bishkek, special forces used dozens of interior ministry troops and armoured personnel carriers to put down one mutiny that had lasted nearly two weeks.
Inmates had taken control of the prison near the village of Moldavanovka in rioting over poor living conditions that swept prisons across the impoverished country on October 20. A parliamentarian and two other people were killed then.
The violence, that was compounded by co-ordinated rioting on Tuesday involving at least five prisons and one detention centre, underscored Kyrgyzstan's political instability following the ouster of President Askar Akayev in March.
President Kurmanbek Bakiyev, who was sworn in August pledging to root out corruption and rampant crime, threatened to sack the government if an investigation into the murder of the parliamentarian in prison found fault with officials.
In the operation against Prison No 31, grenades, submachine guns, rifles and pistols were seized in the jail - a set of drab barracks where inmates were treated for tuberculosis.
Kuvan Mamakeyev, prosecutor for grave crimes, told a news briefing the troops had killed two inmates in Moldavanovka and another two at a jail in Petrovka, about 60 km (37 miles) west of Bishkek. Two inmates were wounded, he said.
Tuesday's protests were well co-ordinated by prisoners using mobile phones, officials said.