Hagel credited the retiring head of the command, Air Force Gen. Robert Kehler, for enforcing tough standards. Kehler began his military career in 1975 as a nuclear missile launch control officer.
Hagel and Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, were at Offutt Air Force Base for the ceremony, as Kehler stepped down and Navy Adm. Cecil D. Haney took the helm.
Last month, Maj. Gen. Michael Carey was fired as commander of 20th Air Force, which is responsible for all 450 of the Air Force's Minuteman 3 nuclear missiles. Carey was fired for behavior that officials have said is linked to alcohol abuse.
His firing and the abrupt removal just two days earlier of Strategic Command's second-in-command -- Navy Vice Adm. Tim Giardina -- for alleged misconduct related to gambling came amid a series of disclosures by the AP about serious security and leadership lapses, morale problems and training flaws. In May the AP disclosed an internal email in which one midlevel nuclear officer said he had found "rot" inside his Minuteman 3 missile unit at Minot Air Force Base, North Dakota.
Air Force and Pentagon officials insist that despite these issues, the nation's nuclear arsenal is being operated and maintained safely.
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Associated Press writer Lolita C. Baldor contributed to this report.