The Freeport school district had relied on the agency's clearance of John O'Mard when he was hired in 2003.
Records showed O'Mard had served almost year in jail after a 1990 conviction for grand larceny and a 1987 petty larceny conviction.
His lawyer said he hadn't yet reviewed the criminal dockets alleging the convictions.
The J.W. Dodd Middle School principal was arraigned Wednesday on a charge of criminal sexual acts.
Police say O'Mard met the 16-year-old boy online in September.