Penates Inc., a nonprofit homeless shelter, owes Suffolk $1,267,471 because the county overpaid for the group’s operations and the agency paid more than budgeted for employee salaries, according to a new audit from Suffolk Comptroller John Kennedy.

The comptroller’s audit, covering the period from April 1, 2008 to March 31, 2013, found the agency not only received $632,858 in excess funding, but paid $610,262 in salaries and fringe benefits that exceeded the budget authorized by the Department of Social Services.

In addition, auditors found the Bay Shore-based agency created a $25,000 capital reserve fund that it did not include as an offset to its revenuers and failed to report $39,813 in payments to clients who could afford sheltering, which should have been returned to the county to offset contract costs.

Kennedy said the county has sent out a letter to the agency demanding repayment in 30 days, but expects the agency to seek a meeting to request a negotiated agreement with a longer repayment schedule.

The comptroller’s audit of Penates was a follow-up to an earlier review from April 1, 2003 to March 31, 2004, which found the agency was overpaid $682,509.

Unlike another recent shelter operator, Long Island Women’s Empowerment Network, which had to be removed earlier this year, Kennedy said Penates cooperated with the audit but “were still deficient” and “did not meet their obligation to be fiscally responsible in delivering the services.” Kennedy added the review along with other shelter audits over the last 20 months have netted the county $6 million.

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In a formal response to the audit, Carolyn Signer, Penates Inc. executive director, said overpayments have “all been recouped directly by Department of Social Services through repayments made from the earlier audit.” She added a “timing difference” that shows overpayments “should be in our favor” as of March 31, 2014.

The comptroller said the money recouped was solely in response to an earlier audit and has no connection to the latest findings.

Signer acknowledged that some employee titles were incorrectly listed, but they were required to provide contracted services and that any added costs were offset by leaving other positions open. She also said unexpected overtime in some cases had to paid as a result of several storms, including superstorm Sandy.