Report by Auditor General Edward Ouko reveals that top officers falsified bills and made payments amounting to millions of shillings.
Ouko reveals that in some instances some firms were recorded as having been paid for food supplies yet they had delivered nothing.
Former Prisons commissioner-general Isaiah Osugo was at the helm during the review period.
The report by Auditor General Edward Ouko details how the department paid phoney suppliers, made double payments for goods and services and procured fake bulletproof vests and jackets.
The audit comes just months after the EACC unearthed an audacious attempt to steal Sh4.8 billion through fictitious security contracts by top prison officials and those in the Interior ministry.
Meanwhile corruption is fighting back.
MPs have accused Auditor General Edward Ouko of systematic flooding of the audit office with members of his ethnic community.
Members of the National and Equal Opportunity Opportunity committee of the National Assembly yesterday hit at Ouko for presiding over tribal hiring contrary to provisions of the Constitution guiding hiring in public offices.