Two of the escapees were serving life sentences on charges of religious extremism and terrorism, while the other two had been charged with the same offences, the prison authority said.
Read: Taliban storm Afghan prison, free hundreds of inmates: officials
Five other prisoners escaped with them, but were later captured, the authority added.
It said three of the four men still at large were members of Jaish al Mahdi, a group which Kyrgyzstan has accused of carrying out several bomb attacks and plotting a coup.
Russia retains a military air base in the Central Asian state, fearing an advance of militantcy in the region. Also closely watching is China, whose restive Xinjiang region borders Kyrgyzstan and which is present in several Kyrgyz industries, including energy and mining.
Read: Kyrgyzstan's security service probes Islamic State recruitment video
Security forces killed six gunmen in clashes in Kyrgyzstan's capital three months ago.
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