The Association to Benefit Children, a nonprofit organization that provides foster-care services, owes the city almost $140,000 for advances it received for foster care during the fiscal 2000 and 2001 years but did not use, according to an audit to be released today by the comptroller’s office.

Typically, the Administration for Children’s Services advances expenses to foster-care services at a per diem rate. In fiscal 2000 and 2001, the agency advanced the association $5.8 million to provide 93,431 days of care in its foster boarding home, 9,396 days of care in its special needs foster boarding home, and 2,037 days-of-care in the Agency Boarding Home, according to the audit. While the days of care were accurate, apparently the per diems were not applied correctly, the report said. As a result, the association should return $139,682 to the agency, the audit found.

The Association to Benefit Children is of particular interest because in 2003 one of the disabled children in its foster care system was found discarded in a trash bag, an action attributed to her foster mother.

The Queens district attorney found that the child died of natural causes, but the episode cast a pall over the city’s foster-care system. Police investigators who visited the little girl’s foster home in Springfield Gardens, Queens, described it as filthy and bug infested.

The office of the comptroller, William Thompson Jr., deals only with the organization’s finances. And in that respect, the audit found the association had fine internal controls over expenses, revenues, and days of care. The reason the association was overpaid was that advance estimates were based on prior-period per diem rates, the comptroller said.

The association agreed with the audit and agreed to repay the city the full amount due.