ALBANY — The state Department of Health squandered $95 million by failing to apply for manufacturers’ rebates on prescriptions paid by Medicaid, state Comptroller Thomas DiNapoli said Thursday.

An audit showed that DOH did not collect savings between Oct. 1, 2014 and March 31, 2015, for emergency-room visits by Medicaid recipients.

DiNapoli said the state has been “missing out on millions in savings to taxpayers and wasting millions more in processing errors.”

He added that state workers also filed inaccurate claims.

The agency has since reclaimed $9.3 million and overhauled policies so the state won’t miss out on ­future rebates.