Only $89,000 has been returned, according to the Illinois Auditor General.
The grant was intended to go toward the rebuilding of Pilgrim Baptist Church, which burned down in 2006.
The findings have sparked new questions about the role Governor Pat Quinn's current Chief of Staff played in the Loop lab school grant.
The 2006 grant agreement was signed by Jack Lavin, who headed the Department of Commerce under Blagojevich and is currently Quinn's Chief of Staff.
