The order, which took effect immediately, says that Worth County Sheriff Jeff Hobby’s administration would be adversely impacted by an indictment issued last month charging Hobby in the incident.
Hobby faces charges of violation of oath by a public officer, two counts of false imprisonment and one count of sexual battery, according to NBC affiliate WALB.
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His lawyer, Raleigh Rollins, did not immediately respond to a request for comment.
The indictment was handed down after the filing of a federal lawsuit alleging that roughly 900 students at Worth County High School were subjected to a humiliating and warrantless search on April 14.
After a series of burglaries, the deputies were targeting 13 students that day, the suit says, but only three came to school.
According to the suit, which was filed by the Southern Center for Human Rights in the U.S. District Court for the Middle District of Georgia, deputies placed the school on lock down for roughly four hours and ordered students to stand spread eagle in the gym.
The deputies then "touched and manipulated students' breasts and genitals" and "inserted fingers inside girls' bras,” the suit alleges, adding that the searches revealed the students’ body parts.
The students felt "fear, embarrassment, stress and humiliation," according to the suit, which is seeking class-action status and a jury trial to decide damages.
Tim Stelloh is a reporter for NBC News, based in California.