Con Edison has overcharged the MTA by millions of dollars on electrical bills over the years, according to a new report.

Transit officials have recouped more than $7 million in overpayments made to the utility giant calculated based on estimates and not actual electricity usage — and the extent of the problem is likely much worse, MTA Acting Inspector General Elizabeth Keating said last week.

“Many MTA electric accounts might have been receiving estimated bills on a long-term — or even permanent — basis,” Keating said in a report Thursday.

“The MTA needs to examine many more accounts for potential overpayments.”

The $7 million accounted in part for payments made to ConEd when the subways closed overnight at the start of the COVID-19 pandemic, the report said.

Estimated bills account for tens of millions of dollars of MTA spending, though the extent to which they utility company has over or under-charged is not fully known. The transportation authority had estimated bills worth $139 million during the period of October 2019 to September 2021, the report said.

A rep for the MTA acknowledged the existence of over-estimated bills, but said the agency has worked to address the issue.

“As older electric meters are replaced, the percentage of estimated bills has declined and continues to trend down. Wherever estimated billing is greater than actual usage, the MTA identifies the difference, proactively requesting and receiving appropriate credits,” MTA spokesman Michael Cortez said in a statement.

ConEd pledged to “work closely with the MTA to help resolve the issues identified in this report.”

“Should billing adjustments be required, they will be done in a timely manner,” said ConEd spokesman Allan Drury in a statement to AM New York.