Darleen Druyun, 56, could be sentenced to as much as five years in prison under the charge of "conspiracy to commit acts affecting a personal financial interest by negotiating employment," according to a Justice Department statement.
The deal to plead guilty to a single criminal information came amid an investigation that could have led to an indictment on additional charges.
Druyun, who was the principal deputy assistant secretary of the Air Force for acquisition and management, helped negotiate the 2002 deal with the Boeing Company to lease 100 Boeing 767 tanker refueling aircraft for the Air Force for more than 20 billion dollars.
She accepted a job with Boeing in January 2003 as vice-president and deputy general manager of the Missile Defense Systems.
Prosecutors said Druyun's daughter, herself a Boeing employee, contacted a senior executive of Boeing in September 2002, setting in motion a process in which Druyun worked out a deal to retire from the Air Force and accept a senior position at Boeing.
"At a time when the government is straining to fulfill its responsibilities with limited resources, it is critical that public officials act with honesty and integrity," US Attorney Paul McNulty said in a statement.
"Darleen Druyun placed her personal interest over the interests of the Air Force and American taxpayers. Secretly negotiating employment with a government contractor, at the same time you are overseeing the negotiations of a multi-billion dollar lease from that same contractor, strikes at the heart of the integrity of the acquisition process."
Druyun was fired last November, along with Boeing's chief financial officer, after details of her job agreement came to light.
Several members of Congress have criticized the tanker deal as too costly compared with the price of purchasing the aircraft outright.
The original plan to lease the 100 tankers ran into trouble over its cost and the viability of leasing, and Congress finally accepted a plan to lease 20 planes and buy 80 to reduce the program's cost.
But some critics of the plan say it should be rebid, questioning whether the European aerospace company Airbus got a fair chance to bid on the contract.
A Senate committee will discuss a series of investigations in early May that could determine the future of the contract.
The Pentagon's inspector general recommended this month that the Pentagon delay the acquisition until serious problems can be corrected.
Boeing said in a statement that the plea agreement related to improper conduct in hiring that the company uncovered itself but not to the tanker program.
"Today's action ... is the result of Boeing voluntarily reporting unethical conduct to the US attorney and other government agencies last November," Boeing said in a statement.
"It is important to note the charge announced today relates to conflict-of-interest in Ms Druyun's hiring and is not related to Boeing business, its financial performance or the 767 tanker program."
Boeing shares fell 94 cents or 2.3 percent to 40.55.