Office spokesman Russ Willard said the investigation began about two weeks ago. He declined to elaborate on the scope.
State auditors found the program marred by fraud, waste and rampant nepotism.
Mr. Perdue introduced the program in 2005 as a way to reward talented teachers who agreed to mentor colleagues in struggling school districts. But none of the $1.2 million set aside by the General Assembly for the program's first two years was used for salary supplements, the audit found.
The audit blasted the former state officials who oversaw the program and the Tennille, Ga.-based regional education agency that ran it. Two state employees were fired; another mentioned in the report left the agency to pursue another position, according to the Georgia Department of Education.
State Schools Superintendent Kathy Cox called for Mr. Baker to investigate the program.
Mike Walker, the director of the Oconee Regional Education Service Agency, has denied any wrongdoing in his organization's handling of its contract with the state to run the program.
"Our records show that all of the funds were disbursed according to the directions and approval of the (state Education Department)," he said in a written statement after the audit's release. Mr. Walker declined further comment Monday.
The state audit found that a state Education Department employee and her family took in more than $170,000 from the program, much of it through improper reimbursements or invoices. The employee also asked other employees to do unnecessary work that was later used in her graduate dissertation about the program.
Mr. Walker steered $53,500 to a company listing his wife as chief executive officer in filings with the secretary of state's office, the report said.
Other former department employees received a slice of the money, though the audit cautions that all of those employees might not have engaged in criminal or unethical activity.
Some of the misappropriated money was used on computer equipment that was seized by the Education Department after it took over the program in the fiscal year that ended June 30. Auditors found personal photos and pornography on some.
Reach Brandon Larrabee at (678) 977-3709 or firstname.lastname@example.org.