Conner is now the town manager of Atlantic Beach, South Carolina.
Thursday a Horry County grand jury indicted her on the two counts of misconduct in office and one count of violation of employer's obligation to a police retirement fund.
The town's mayor was also indicted.
Conner is also accused of illegally using money for the retirement account for other town expenses. She has until Monday to turn herself in to authorities.
In 2004, Conner was forced to resign as Durham city manager after a series of missteps.