The New York Department of Health made $32.9 million in Medicaid overpayments during a five-year period, according to audits released by state Comptroller Thomas DiNapoli.
The overpayments were due mainly to the issuance of multiple identification numbers to Medicaid recipients.
A third audit found $24 million in missed savings for physician-administered drugs.
"Due to a lack of basic oversight, overpayments such as these continue to plague the system," DiNapoli said.
The comptroller's office has issued numerous audits identifying problems with eMedNY, the DOH claims-processing system.
Through eMedNY, Medicaid claims are subject to automated checks or edits that determine whether the claims are eligible for reimbursement.
The comptroller has recommended that the DOH move to recover funds where possible and take immediate steps to prevent the issuance of multiple identification numbers.