The New York City Housing Authority squandered repeated opportunities to collect hundreds of millions in federal subsidies — and ignored a report it commissioned on how to cut costs, according to an audit released Wednesday.

City Comptroller Scott Stringer said the agency failed to secure $353 million in federal energy incentives and lost $263 million by not moving 8,400 apartments into the federal Section 8 program.

He also said it hired Boston Consulting for $10 million for a study on cost savings, but never followed up on the company’s recommendations, which could have saved $106 million.

Stringer’s audit covered a period before the de Blasio administration took office.

The agency responded, “The audit . . . uses outdated facts and alarmist, unrealistic figures.”