Ackerman, whose salary is $348,000, received a $65,000 bonus last year. She recently announced she would defer a $100,000 bonus due her after June 30 until the district's budget became clearer. She also said she would take 20 furlough days.
While noting the furloughs, the audit letter added, "we firmly believe that the SRC should not have allowed such generous terms in her employment contract, especially performance and retention bonuses."
In a statement, School Reform Commisssion Chairman Robert L. Archie praised Ackerman for leading the district to "tremendous academic strides" and dealing with its fiscal challenges.
The district, which operates on a $3.2 billion budget, is facing a deficit of at least $465 million in the fiscal year that will begin July 1. Some knowledgeable sources have said the funding gap exceeds $600 million.
Addressing the audit, Michael Masch, the district's chief financial officer, said the issues were being "attacked aggressively and being solved by the current administration."
The audit said the district failed to adequately provide information on its enrollment and attendance on which state subsidies are based. Wagner said that the district had improved its record-keeping but that problems - which have occurred for decades - remained.
The district received $4.2 billion in state subsidies from 2004-05 to 2007-08, and the audit said it could not determine whether the funding had been appropriate.
Masch acknowledged problems but said the district had taken significant improvement steps that the auditors did not want to review.
Contact staff writer Susan Snyder at 215-854-4693 or ssnyder@phillynews.com.