An audit by state Comptroller Tom DiNapoli found New York’s Medicaid program duplicated payments to the tune of $102.1 million over four years.

Auditors found that between 2014 and 2018, the state Department of Health made payments for managed-care premiums to 65,961 individuals with multiple client identification numbers.

The mix-up stemmed from missing or incorrect Social Security numbers and wrong addresses.

“System flaws and incorrect or incomplete information have caused duplicate Medicaid premium payments for a long time,” DiNapoli said. “The Department of Health needs to do a better job coordinating with all stakeholders in the Medicaid system to eliminate this waste, improve efficiency and streamline communication.”

DiNapoli also noted further complication thanks to the lack of a centralized system between New York City and upstate Welfare Management Systems and the New York State of Health system, established under ObamaCare.

DOH said it’s working to fix the mistakes. “The department recently allocated additional resources to duplicate research and resolution and created a unit for this purpose,” the agency said of the findings.

Bill Hammond, director of health policy for the Empire Center, was critical of the bungling.

“A little series of mistakes in a program this big can add up to a lot of money in a hurry,” Hammond told The Post. “A quarter of a million dollars is a lot of money. It’s important that the auditors are looking at this and are pointing to things that could be fixed.”

In fiscal year 2017-2018, the state’s Medicaid program had 7.3 million total recipients and $62.9 billion in total claim costs.