Planes in Iraq and Afghanistan and planes participating in air shows this weekend are not affected by the stand-down.
While airmen haven't been given specific instructions for the stand-down, they've been ordered to take the non-flying time to review safety procedures and protocol, an Air Combat Command spokesman said.
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On Aug. 30, a B-52 with six nuclear-tipped cruise missiles flew from Minot Air Force Base, N.D., to Barksdale Air Force Base, La., a military official told The Associated Press.
The missiles, which are being decommissioned, were mounted onto pylons on the bomber's wings.
It is unclear why the nuclear warheads had not been removed beforehand.
The plane's crew, according to news reports, did not know they were carrying nuclear weapons.
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The munitions squadron commander was relieved of duty, and crews involved with the load have been temporarily decertified for handling munitions, an official told the AP.
Citing Defense Department policy forbidding the release of any information about nuclear weapons, Pentagon officials have not confirmed that nuclear weapons were involved in the incident.
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Gates has asked to be briefed daily on the Air Force investigation, which is being led by Air Force Maj. Gen. Douglas Raaberg, director of Air and Space Operations for Air Combat Command at Langley.
Raaberg was not available for comment Thursday.
His full report is expected to be delivered to Gates as early as next week.