Officials in the office said little about why she fired Tim Wheeler, who has worked for the department since December 2001.
"The clerk is making some changes in the office and this is one of them," said Randy Kenner, the department's managing clerk.
As chief deputy, Wheeler technically operated as Shanks' second-in-command. He earned almost $82,000 annually.
Responding to his termination, Wheeler on Friday night said he'd enjoyed his job, which he thought he did "extremely well," and was disappointed to be losing it.
He said Shanks had recently been missing work. He said he told her judges and others in the court system had been seeking his help in her absence.
"I told her about these requests because I was truly concerned about the damage to the office and to the Clerk's reputation from her neglecting her duties. I felt it was my job to make sure the office continued to run in her absence," his letter states.
He added that while he was away on a leave of absence caring for his dying father that Shanks began acting erratically, resulting in the departures of several employees. According to Wheeler, she filled the vacancies with friends and acquaintances who weren't qualified for their jobs.
Kenner said Shanks, whose office also oversees Juvenile Court, has no plans to fill the position at this point.
Wheeler was a Knoxville City Council candidate in 2003