The Economic Development Corporation left millions of dollars intended for public projects — including $8.9 million for the restoration of a waterfront site in the South Bronx — sitting unused for decades, an audit from the Comptroller’s office found last week.

The so-called “Public Purpose Funds,” were obtained by the city from private corporations in exchange for tax breaks. The money, $9.3 million, has been managed by the EDC in accounts that have seen no activity for years, according to a report released by Comptroller John C. Liu.

“It makes little sense that millions intended for economic development remain unused for so long, especially in the Bronx where jobs are greatly needed,” Liu said in a statement.

“If the EDC can’t figure out how to put the capital to work, then at least return the money to the city treasury.”

Money for the Bronx project was acquired by the EDC in 1992. The funds were designated to develop rail freight traffic at the Harlem River Yards, an unutilized 96-acre site in Mott Haven. Though the land was leased to the private company Harlem River Yard Ventures, Inc., the money has yet to be disbursed.

The project has “no foreseeable future,” according to the report. Liu’s office recommends that the money either be repurposed for something else or given back to the city.