"The allegations are not related to operational readiness or the inspection results of any 20th AF unit, nor do they involve sexual misconduct," service officials claim.
The three service wings within the 20th Air Force "provides on-alert, combat ready ICBMs" options to the White House and Pentagon, according to the statement.
"20th AF continues to execute its mission of around-the-clock nuclear deterrence in a safe, secure and effective manner," Kowalski said Friday.
"It's unfortunate that I've had to relieve an officer who's had an otherwise distinctive career spanning 35 years of commendable service," he added.
On Wednesday, the three-star admiral who is the No. 2 official in charge of the U.S. nuclear forces was fired in the wake of a Naval Criminal Investigative Service gambling probe.
A National Security Council spokesman confirmed that President Obama relieved Vice Adm. Tim Giardina from his post as deputy commander at U.S. Strategic Command on Oct. 3.
Giardina was quietly suspended last month as a result of the NCIS investigation that he allegedly used counterfeit gambling chips at an Iowa casino.
Giardina was named the No. 2 official at Strategic Command, which overseas the U.S. nuclear arsenal, in December 2011.