Derrick Wooten was indicted Tuesday on four counts of public record fraud, four counts of criminal attempt to commit a felony and one count of computer forgery.
A DeKalb judge signed a warrant for his arrest.
Wooten was working as an assistant principal at Stoneview Elementary in Lithonia when he instructed eight teachers to change students' attendance records on a school computer, District Attorney Robert James told The Atlanta Journal-Constitution.
"He is accused of changing attendance records to reflect children were in school when they weren't. This was all to make it look better for AYP," James said Tuesday. "The motive was to cover this up so the school doesn't get put on the Needs Improvement list."
Wooten was one 24 educators yanked from the classroom in January as part of a probe into allegations of cheating on the CRCT test. Wooten is not accused of irregularities with the standardized test, but the internal CRCT investigation uncovered the attendance altering, district spokesman Walter Woods said.
As of Tuesday, Wooten, an employee since 2007, remained with the school system in an administrative position, Woods said.
"The district attorney's actions show the seriousness of the actions alleged. The school district supports true academic achievement accomplished by quality teaching," Board Chairman Tom Bowen said. "We do not condone unethical or illegal steps to overstate performance. Such behavior is dishonest to students and deprives them of the opportunity to learn."
In addition to the criminal investigation, the Georgia Professional Standards Commission is investigating Wooten's teaching certificate, Woods said.
James said the CRCT investigation is still ongoing.