Major General Michael Carey was relieved of his command of the 20th Air Force, responsible for maintaining "on-alert" intercontinental ballistic missiles, because of "a loss of trust and confidence in his leadership and judgement," spokesman General Les Kodlick told reporters.
Carey is the second senior officer in the nuclear command to be fired this week. The deputy commander of the country's nuclear forces, Vice Admiral Tim Giardina, was sacked two days ago after he came under investigation for allegedly using counterfeit chips at a casino in Iowa.
The spokesman would not reveal the nature of the misbehaviour pending the outcome of the investigation but said it did not involve sexual misconduct or criminal activity.
The misbehaviour occurred during a work trip but officials would not provide further details.
Officers said Carey was not being sacked for any conduct related to the readiness of the 20th Air Force unit at F.E. Warren Air Force base in Wyoming or to recent failed inspections for some missile units.
"It's unfortunate I've had to relieve an officer who has had an otherwise distinctive career spanning 35 years of commendable service," he said.
The vice commander of Air Force Global Strike Command, Major General Jack Weinstein, was named as the interim commander of the 20th Air Force unit.
The military's nuclear command has come under growing scrutiny in recent years after a number of blunders and critical inspections.
The nuclear missile unit at Minot Air Force Base in North Dakota earlier this year disciplined 17 launch control officers after an inspection uncovered problems and later relieved an officer who oversees training.
In 2008, then defense secretary Robert Gates sacked the Air Force secretary and chief of staff, blaming them for what he called an erosion of standards that led to two mistakes involving nuclear weapons.