Education Department spokesman Timothy Eller said the department, which has an $11.2 billion budget, welcomed an audit of its operations.
"The department believes that the auditor general will find that the department is dedicated to ensuring that all students are provided with quality educational opportunities, and under Gov. Corbett, the department has implemented initiatives necessary to raise student achievement and prepare today's students for the jobs of tomorrow," Eller said in a statement.
DePasquale, a Democrat, said that during his first year in office, his staff completed more than 300 school audits statewide. It found no problems or only minor infractions at most schools and more serious problems with others.
"In the worst cases, we found wasted money that should have gone toward classroom education," he said.
DePasquale cited lavish salaries and buyout packages for some superintendents. He said he was particularly concerned about widespread problems found in a state program that gives charter schools partial reimbursement for rental costs.
Auditors found that several charter schools were not entitled to the state funds because they were renting facilities owned by related entities.
"A lot of money is going out the door," he said.
In August, his office said that Chester Community Charter School had received more than $1.2 million in improper lease reimbursements over three years because it had participated in a "circular lease arrangement among related parties."
While Chester Community disputed that finding, DePasquale said officials from the other charters had thanked him for highlighting the issue.
"They didn't know they weren't allowed to do this," he said.
DePasquale said that when he pointed out the problem, Education Department officials told him there was no staff to collect and examine charter-school leases.
Eller disputed that. "Every request for a charter-school lease reimbursement is reviewed by department staff," he said.
DePasquale, who just completed his first year as the state's top fiscal watchdog, said some of his predecessors had reviewed the performance of specific education programs, but he said the scope of his review would be broader.
He also said his office was scheduled to begin a regular audit of the Philadelphia School District in April. The last was done in March 2011.
DePasquale, who has announced that he will conduct a series of meetings on charter-school accountability in February and March, said he had added a Philadelphia session to the lineup. No date or location has been set for that meeting.
Earlier in the day, DePasquale visited the Freire Charter School in Center City. He said that of the 15 charters his office audited in the last year, the school with 1,000 students in grades five through 12 received the highest marks.