WASHINGTON—Defense Secretary Robert Gates ousted the Air Force’s top military and civilian leaders Thursday, holding them to account in a historic Pentagon shake-up after embarrassing nuclear mix-ups. Gates announced at a news conference that he had accepted the resignations of Air Force Chief of Staff Gen. Michael Moseley and Air Force Secretary Michael Wynne—a highly unusual double firing.

Gates said his decision was based mainly on the damning conclusions of an internal report on the mistaken shipment to Taiwan of four Air Force electrical fuses for ballistic missile warheads. And he linked the underlying causes of that slip-up to another startling incident: the flight last August of a B-52 bomber that was mistakenly armed with six nuclear-tipped cruise missiles.

The report drew the stunning conclusion that the Air Force’s nuclear standards have been in a long decline, a “problem that has been identified but not effectively addressed for over a decade.”

Gates said an internal investigation found a common theme in the B-52 and Taiwan incidents: “a decline in the Air Force’s nuclear mission focus and performance” and a failure by Air Force leaders to respond effectively.