The removal was not linked to the operation of the nuclear arsenal, which was safe, the officials insisted on Friday.
On Wednesday the US Navy announced an admiral overseeing nuclear weapons forces had been sacked from the role.
That was due to illegal gambling activities, officials said.
Michael Carey is a two-star general in the 20th Air Force and was responsible for maintaining intercontinental ballistic missiles (ICBMs) at three bases across the US - a total of 450 missiles.
In a statement, the Air Force said Lt Gen James Kowalski, the commander of Air Force Global Strike Command, had made the decision.
It reads: "Kowalski made his decision based on information from an Inspector General investigation into Carey's behavior during a temporary duty assignment.
"The allegations are not related to operational readiness or the inspection results of any 20th AF unit, nor do they involve sexual misconduct."
Gen Kowalski oversees all Air Force nuclear weapons, including aircraft-delivered.
The vice commander of Air Force Global Strike Command, Maj Gen Jack Weinstein, is temporarily replacing Gen Carey.
RA/NJF