An embattled nonprofit homeless shelter operator linked to a Bronx radiator accident that left two children dead used money meant for needy New Yorkers to inflate executive salaries, The Post has learned.

A top official at the Bushwick Economic Development Corporation paid himself as much as $651,000, even as his nonprofit failed to pay rent on its shelters and fix dangerous safety issues.

The massive salaries came “while the organization’s clients, programs and overall fiscal health suffered,” the Department of Investigation determined in a report obtained under New York’s Freedom of Information Law.

“DOI’s investigation revealed large, undisclosed salary payments to top BEDCO executives at a time when the organization was failing to pay its debts to landlords (thus potentially jeopardizing the security of the housing for City clients), as well as to cure significant safety violations in its buildings (thus potentially jeopardizing the safety and well-being of those same clients),” the watchdog’s damning 13-page investigative report concluded.

DOI investigators determined BEDCO’s brass hid their paydays from the charity’s board — and on filings made with city and federal authorities.

Records obtained by city inspectors showed that BEDCO’s executive director Frank Boswell paid himself $651,292 in 2016.

That’s triple the $194,213 the nonprofit reported on its filings to the U.S. Internal Revenue Service, known as a ‘Form 990.’

DOI also found that the nonprofit’s chief financial officer, Keith Walker, scored $485,541 in 2016; its operations executive, Douglas Wood, made $383,429; and even the bookkeeper, Kanta Lachman, banked $332,276.

The sky-high executive salaries were paid for entirely with tax dollars because BEDCO’s only revenue came from city contracts, investigators said.

“BEDCO consistently underreported the amounts of these salaries on official forms,” including filings with DHS, the investigation also found.

Boswell declined to comment Friday when approached by a Post reporter at his Brooklyn office.

The top-dollar executive payouts came while BEDCO shirked rent and maintenance on its traditional shelter facilities — endangering New York’s vulnerable, records show.

DOI found that BEDCO neglected key safety and maintenance needs at the two traditional shelters where it was responsible for upkeep.

Inspectors from the city’s Buildings Department and Environmental Review Board hit the two facilities with a combined 80 violations between 2013 and 2018 — most of which remained unfixed, DOI found.

In one building, city inspectors discovered an improperly grounded electrical system and a blocked passageway to an exit.

Officials hit another shelter with a violation because it lacked a required automatic sprinkler system to protect residents in case of a fire.

BEDCO’s short-shrift even extended to paying rent.

Three of the nonprofits landlords separately dragged to court in 2016 and 2017 over claims it failed to at least $5.4 million in rent, DOI found.

Additionally, The Post identified a fourth case in Brooklyn where BEDCO fell behind on at least $1.1 million in rent for a Crown Heights building, nearly resulting in the eviction of the shelter’s tenants.

DHS shut down the Brooklyn shelter and relocated the residents after inquiries from The Post about the case.

BEDCO currently operates two traditional shelters.

That’s just a fraction of the work BEDCO once scored from DHS as the city’s homelessness crisis exploded.

DHS gave BEDCO $31 million in 2015 to run a sprawling operation that included six traditional shelters, hotel rooms and apartments scattered in buildings across the city.

Many of the contracts were approved on an emergency basis, which DOI found did not have the same safeguards against misuse of funds — laying the groundwork for Boswell’s scheme, DOI found.

“DHS did not restrict the percentage of those fees that BEDCO executives could use for their salaries,” investigators found. “As a result, there were effectively no controls — such as reporting on budget forms — to prevent large portions of these funds from being allocated to executive compensation, rather than building maintenance and other program expenses.”

BEDCO came under intense scrutiny in December 2016 after a steam leak from a busted radiator in a Bronx apartment scalded two young children to death.

Following the horrifying accident, city officials said they would move BEDCO’s operations to other providers and reexamine DHS’s relationship with the troubled nonprofit.

But unwinding the group’s contracts proved more complicated than expected, officials said.

After questions from The Post, DHS officials told the paper they plan to finally close down the nonprofit’s last two shelters by the end of the city’s current budget — June 30, 2020 — and move tenants to other locations.

“As part of our effort to transform the shelter system, this provider is being phased out,” said spokesman Isaac McGinn.

The embattled agency also says it tightened reporting rules and is moving away from the emergency contracts that DOI found BEDCO executives exploited.

“We’ve implemented strengthened fiscal protocols and are closely monitoring compliance to ensure no corners are being cut,” McGinn added.

Additional reporting by Israel Salas-Rodriguez, Khristina Narizhnaya, and Georgett Roberts