The report, completed in May but made public Monday, also faulted agency CEO John Matheussen for not telling Gov. Chris Christie's liaison to the DRPA about the pay hikes last year.
Mathuessen says the report from agency Inspector General Thomas Raftery is misleading.
The DRPA runs four Philadelphia-area bridge connecting New Jersey and Pennsylvania and the PACTO commuter rail line.
Officials from both Pennsylvania and New Jersey have been critical of the agency's practices.
Details of the audit were first reported by The Courier-Post of Cherry Hill.
Information from: Courier-Post (Cherry Hill, N.J.), http://www.courierpostonline.com/