The New York City Housing Authority failed to properly maintain its roofs — and wasted millions on repairs because staffers had no clue they were covered under warranty, a new Comptroller’s report finds.

“At a time when saying every penny counts, NYCHA is essentially lighting money on fire by investing millions in roof repairs when it doesn’t have to,” City Comptroller Scott Stringer said at the Ingersoll Houses in Brooklyn.

“The buck stops in the Mayor’s Office and I respectfully say to the Mayor: ‘Enough already. You got to fix this. This is a management issue,” he added.

Inspectors from the Comptroller’s Office found that NYCHA failed to properly maintain 19 of the 35 roofs they checked at 13 of the authority’s developments.

“The deficiencies included ponding water, soft and spongy spots, blisters, sagging roof conditions, open seams at the edges of the base flashing on rooftop structures and damaged masonry,” the audit found.

The failures provide ideal conditions for toxic mold to grow in buildings, it added.

NYCHA is under a court order to clean the mold out of apartments, but has struggled to complete repairs because of leaky roofs and aged pipes that are prone to bursting.

The Comptroller’s report stretched for 62 pages.

Inspectors found NYCHA staffers performed unauthorized repairs that did not comply with the roof’s warranties — and that two-thirds of the managers interviewed were unaware their roofs were even covered.

Additionally, NYCHA failed to track maintenance, repairs and warranty paperwork.

“NYCHA’s roof-related record-keeping — both in hard copy and on its IT systems — which is necessary for the effective tracking of roof maintenance and repairs, and for preservation of NYCHA’s roof-warranty coverage, was inadequate,” the report found.

The Comptroller’s office discovered one case where NYCHA spent $3.7 million to replace eight roofs at Staten Island’s South Beach Houses — even though they should have been under warranty for another decade.

The cash-strapped agency made “no discernible effort” to invoke the warranty and couldn’t explain why it didn’t try.

Overall, NYCHA used its warranties to cover just nine of the 709 eligible roof-related repairs between 2009 and 2017.

“The Comptroller’s audit and recommendations are consistent with what the Authority has been aware of and addressing through new systems we are already implementing,” claimed NYCHA rep Chester Soria.

Stringer’s report is the housing agency’s latest headache.

Federal monitor Bart Schwartz released a report Monday that revealed new NYCHA dysfunction, including a spewing drainage pipe at Harlem’s Polo Grounds Towers that went unrepaired for two months for want of a ladder.

NYCHA was partly taken over by the feds as part of a January settlement after prosecutors alleged officials lied for years about lead inspections and unsafe living conditions.