Jail superintendent Ashish Tiwari has registered an FIR against 250 inmates, including 106 named inmates, late last night, said Circle Officer (Cant) Raj Kumar Yadav.
An inquiry was going on, he added.
Tiwari was taken hostage while his deputy Ajai Rai seriously injured as inmates clashed with staff and took control of a section of the prison barracks yesterday.
The jail superintendent was taken hostage by the inmates, who were unhappy over several issues, including the "poor quality" of food served at the prison.
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The inmates had gone on the rampage yesterday after two of their prison mates were allegedly beaten up by guards.
As the inmates clashed with jail officials, Deputy Jail Superintendent Ajay Rai received serious injuries while several prison guards, too, were assaulted, police sources said.
DM Raj Mani Yadav, senior prison department officials and an NDRF team went to the jail to deal with the situation.
Both the Jail Superintendentand his Deputy were replaced with immediate effect following a demand by the inmates.