Donley, who was acting secretary of the Air Force for seven months in 1993 and served as the service's top financial officer from 1989 to 1993, would replace Michael Wynne, who was fired by Gates on Thursday along with the Air Force's top uniformed officer, Gen. Michael Moseley.
The senior defense official spoke on condition of anonymity because Gates has not yet made a formal recommendation to Bush.
Donley currently is the Pentagon's director of administration and management.
He has held a variety of strategy and policy positions in government, including a stint on the National Security Council from 1984 to 1989. Before that he was a member of the Senate Armed Services Committee staff. He served in the Army from 1972 to 1975.
Gates announced on Thursday that he was replacing the Air Force's top leadership, saying a shakeup was required to ensure that the service improve its standards and performance in safeguarding its nuclear weapons and the sensitive components associated with the strategic arsenal.
Gates said at a news conference that he had accepted the resignations Moseley and Wynne - a highly unusual double firing, reports CBS News correspondent David Martin.
"I believe these actions are required because … the focus of the air force leadership has drifted with respect to perhaps its most sensitive mission," said Gates.
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.
In a reflection of his concern about the state of nuclear security, Gates said he had asked a former defense secretary, James Schlesinger, to lead a task force that will recommend ways to ensure that the highest levels of accountability and control are maintained in Air Force handling of nuclear weapons.
In somber tones, Gates told reporters his decision to remove Wynne and Moseley was based on the findings of an investigation of the Taiwan debacle by Adm. Kirkland Donald. The admiral found a "lack of a critical self-assessment culture" in the Air Force nuclear program, making it unlikely that weaknesses in the way critical materials such as nuclear weapons are handled could be corrected, Gates said.