Anthony J. McNeil, 54, was fired from his job Oct. 10 after lottery officials discovered accounting discrepancies, The State, Columbia, S.C., reported.
He is accused of manipulating the agency's computer system to overcharge some ticket retailers and not charge others, a lottery affidavit states.
The affidavit said McNeil would call the retailers that weren't charged and instruct them to deposit payments into an account he controlled.
Lottery Director Paula Harper Bethea said the irregularities occurred over a two-year period and did not affect lottery players or prizes.
"Although the tightest internal controls were in place, McNeil was intent and found a way to circumvent procedures," Bethea said.