Stan Butkus' departure came nearly three months after a state audit found the Department of Disabilities and Special Needs falls far short in protecting South Carolina's most vulnerable children and adults.
Criticisms in the Dec. 2 report included failure to follow up on safety violations and not doing enough to keep abusers off facility payrolls.
The board that oversees the agency accepted Butkus' resignation Friday, his last day. Butkus did not immediately return a message at his home seeking comment.
"Dr. Butkus has done an outstanding job for our state and department in many ways. He is innovative and also willing to make the really tough decisions," board chairman Bobby Harrell of Yemassee wrote in his announcement, dated Friday, to agency employees, providers and families. He is no relation to House Speaker Bobby Harrell of Charleston.
"Dr. Butkus is a skilled professional and a faithful public servant. We wish him the very best," the board chairman wrote.
While Harrell said he made the announcement with regret, he added the timing was right for Butkus to leave.
Gov. Mark Sanford told the commissioners they should consider firing Butkus.
"Given what was suggested in the audit, it was clear a change of leadership was needed," Sanford spokesman Joel Sawyer said.