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The Suffolk comptroller’s office has begun withholding a $20,000 monthly check to homeless shelter provider Haven House/Bridges after an audit earlier this summer found the nonprofit owed the county $540,000.

Comptroller Joseph Sawicki said Suffolk began dunning the agency because its proposed repayment offer amounted to only $300,000 over three years.

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Sawicki’s audit found that Haven House billed the county for workers who were allowed to sleep on the job,  use of buildings not in county programs, and rental and upkeep of luxury cars for the group’s head.

County social services officials agreed with the conclusions. Bruno LaSpina, Haven House chief executive, said the organization is still in discussions with the county and declined to comment while talks are going on. Sawicki is withholding about 10 percent of Haven House’s monthly payment. That will result in the county recouping its money within 27 months, said chief deputy Christina Capobianco.