Federal prosecutors and the city Department of Investigation raided the offices of Childrens Community Services, the city’s $600 million hotel shelter operator, as they probe allegations that executives bilked taxpayers from millions in fraudulent billings.

The bombshell disclosures were contained in a lawsuit filed Wednesday by the Department of Homeless Services in Manhattan Supreme Court, which alleges the fraud constitutes a breach of contract and asks a judge to appoint a receiver to take over the operation.

In the filing, city officials linked the fraud scheme to two top CCS officials, Thomas Bransky and Ruth Mandelbaum — the nonprofit’s chief executive and chief operating officers.

“CCS and its top officials, Bransky and Mandelbaum, engaged in fraudulent billing and invoicing practices that put in jeopardy the approximately 1,900 households… served by CCS in connection with the City’s mandate to provide shelter,” DHS charged in the lawsuit.

The lawsuit also revealed that a series of addresses linked to CCS and its subcontractors were raided Monday by DOI and Manhattan federal prosecutors.

Both agencies declined to comment.

DHS officials would not reveal how much taxpayer money the nonprofit’s executives allegedly stole.

Commissioner Steven Banks said late Wednesday the total runs into the “millions” and that the agency has withheld sufficient funds from CCS to recoup the losses.

It’s a stunning turn of fate for CCS, which scored its first city business in 2014 and then grew at an astonishingly quick rate to become one of New York’s largest hotel shelter operators.

All told, the nonprofit provides shelter to 1,900 families across the city, most of whom are living in the city’s embattled hotel shelter system. CCS holds $600 million in hotel contracts alone, city contract records show.

The 29-page court filing claims that CCS often sat on both ends of the transactions that allegedly put money into the hands of its current and former top brass.

A former CCS board member, Peter Weiser, directly or indirectly controls at least four of the CCS vendors named in the lawsuit.

Weiser and Mandelbaum — CCS’s chief operating officer — have a history that dates back at least two decades, clippings show.

The pair were codefendants in a settled 1997 federal lawsuit that alleged Weiser attempted to bribe Rubbermaid employees on behalf of a medical supplies wholesaler, Crain’s New York reported in 2018.

CCS hired one Weiser-connected company, AMX, to provide appliances for a now-shuttered shelter operation once housed in a Bedford-Stuyvesant apartment building.

The firm was headquartered out of a fourth-floor Harlem apartment and maintained no store or warehouse, officials discovered.

The nonprofit could not prove it bid out the work as is required under the city contract and the price list provided to DHS was “created by CCS… just minutes before CCS sent it” and contained numerous typographical errors including spelling freezer, “frezzer.”

CCS picked another Weiser-linked firm, AZ, to maintain its computers and other office equipment. But the business was based out of a Nassau County post office box and maintained “no other known location suitable for the provision of services detailed in CCS’s subcontract.”

When quizzed by DHS staff, Bransky said he could not locate bids from other providers to prove the nonprofit complied with city contracting requirements.

The Post has highlighted the shoddy and dangerous conditions in CCS’s hotel shelter operations. But, city officials said Wednesday that the decrepit conditions could not be directly linked to the allegations of theft.

Bransky, Mandelbaum, CCS’s attorney and a spokesman for the nonprofit all did not respond to requests for comment.

– Additional reporting by Andrew Denney, Priscilla DeGregory and Emily Saul