After nearly three decades of funding the Amboy Neighborhood Center in Brownsville, Brooklyn, to run an emergency shelter for homeless families, the city is searching for a new program manager after a series of audits accuse the group of mismanaging money and its property in recent years.

In June, City Comptroller Bill Thompson charged Amboy with running a facility with “deplorable conditions” like clogged sinks, roach and rat infestations, broken windows and chipping plaster, after his office conducted an audit of 51 of the group’s 224 apartments. The findings were nothing new: A year earlier, Thompson’s predecessor, Alan Hevesi, chastised the city Department of Housing Preservation and Development for placing “families, some with small children, in apartments unfit for human habitation.”

For 28 years, HPD has had an annual contract — worth $4.1 million last year — with Amboy to provide temporary emergency housing and supportive services to families that lost their homes to fires, or to vacate orders issued by the Department of Buildings, the Fire Department or HPD’s own code enforcement staff. Amboy, a 13-building complex, is one of four such facilities that HPD funds.

In response to Thompson’s audit, Amboy administrators claimed they did not receive enough money from the city to adequately maintain their buildings. But Thompson’s study questions those claims: The group, which is a subsidiary of the century-old nonprofit Colony-South Brooklyn Houses, had $484,968 in the bank at the time of the audit. The comptroller’s office also questioned a $135,433 management fee that Amboy paid to Colony-South since, said the audit, there was no contract between the two groups “indicating what services were to be rendered.”

In recent weeks, HPD has begun shopping around for a new manager. An agency spokesperson told City Limits that the decision has nothing to do with the audits: “Amboy Neighborhood voluntarily and willingly asked to step out of their management role… They have refused to sign an official contract.”

Officials at neither Amboy nor Colony-South responded to detailed questions from City Limits about the audits or their upcoming loss of the HPD contract. However, in a written response to the comptroller, Amboy’s board of directors accused HPD of seeking to “cripple and euthanize the Amboy Shelter operation financially” by delaying and reducing their payments. The board also blamed “the dysfunctional behavior of a significant number of families” for their living conditions.

Finding someone to take over these buildings may be a tough sell. Pointing to the size of the project and the families who live there — many are large — Fred Shack of HELP USA, one of the city’s largest homeless service and housing providers, said, “There are clearly some challenges.” HPD recently asked HELP USA to apply to take it on. The group, said Shack, is still thinking it over.