ALBANY — New York’s $721 million Medicaid billing computer program is failing to catch overpayments, duplicate billings and fraud, costing the state millions, comptroller Thomas DiNapoli said.

In an audit released Wednesday, DiNapoli said he found $1.8 million in health care overpayments through the computer program, eMedNY, from 2006. That’s part of an overall loss that year of $63 million.

It’s not much compared to the multibillion dollar state deficit, but DiNapoli said the problem demonstrates a systemic lack of oversight that costs taxpayers money in the long run.

New York spends about $42 billion a year on Medicaid.

“Our auditors continue to find systemic problems with the Department of Health’s Medicaid claims processing system,” DiNapoli said. “Questionable claims keep slipping through.”

The comptroller’s office said the health department’s system for oversight and monitoring information technology is lacking, and some of the employees charged with monitoring the program don’t clearly understand how it works. DiNapoli called for better training.

Health officials said they’re acting on the comptroller’s recommendations and are always pursuing collection of inappropriate payments and refining the process for catching Medicaid fraud and errors.

“There’s no doubt that any computer system will not be perfect,” said Claudia Hutton, a spokeswoman for the Department of Health. “And there’s no doubt there are innumerable ways that people will try to break the rules. For every time we fix certain things, there will be another set of things we have to fix. It’s just life, but we don’t take it cavalierly.”

The health department also doesn’t have a process for prioritizing and approving computer program changes to eMedNY, according to DiNapoli’s report. Instead, the agency often relies on “who complains the loudest” to determine the most urgent request to fix programming errors.

Some of the flaws the audits have found in the past seemed obvious — for example a dentist who billed Medicaid for providing seven patients with 32 fillings each and then later for pulling the same 32 teeth for each patient. The billing system didn’t catch that error. The system has been corrected to catch similar filings, and that dentist was kicked out of the Medicaid program.

The eMedNY system automatically checks claims and edits to determine whether the providers are eligible for reimbursement. It’s designed to detect duplicate bills, or unnecessary and uncovered procedures.

The program can deny or suspend a claim. But in some cases the automated edits in eMedNY were not properly set up, not set up at all, or not functioning as intended.

“At a time when state and local governments are facing record deficits, we have to scrutinize all spending and use every tool available to detect fraud and billing errors,” DiNapoli said.