Mukeyev has headed Kyrgyzstan's jail system since taking over after a wave of deadly prison riots in October.
He said he was dismissed after investigators found he had authorized paying too much for a recent supply of barbed wire for prisons under his control.
A spokesman for the Kyrgyz general prosecutor's office said Mukeyev was accused of "misuse of power over barbed wire purchases."
The Kyrgyz law-enforcement and security sector has been the object of intense scrutiny since Prime Minister Feliks Kulov on 25 January publicly accused police and security forces of failing to curb organized crime and corruption. Fallout has included the resignations of senior security officials.