Deputy Defense Secretary William J. Lynn III has resigned as the Pentagon’s No. 2 official, shortly after Leon E. Panetta was installed last week as the new defense secretary, the Pentagon said on Thursday.
“I thought this was a logical point for me to depart the Pentagon,” Mr. Lynn told the Associated Press, which first disclosed the resignation.
A Pentagon statement gave no reason for Mr. Lynn’s departure but said he would remain in the post until this fall when a successor is in place.
Mr. Lynn told AP he was leaving for “personal, family reasons” unrelated to being passed over for the defense secretary post.
Mr. Lynn, who has served as the deputy secretary since February 2009, submitted his resignation to Mr. Panetta last Friday, on the new secretary’s first day in the Pentagon.
“Bill Lynn has provided outstanding advice and counsel to this department and to the nation over the course of his long career,” Mr. Panetta, until recently the CIA director, said in a statement. “His service will be greatly missed.”
Mr. Lynn said he was resigning for personal reasons and because he could not commit to serving as deputy secretary until 2013, the end of President Obama’s first term.
The announcement follows a string of departures and promotions within the Pentagon, following the retirement of former Defense Secretary Robert M. Gates last week.
Gen. David H. Petraeus, until recently commander of U.S. and allied forces in Afghanistan, replaced Mr. Panetta at CIA.
Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, will end his term on Oct. 1, and Army Chief of Staff Gen. Martin E. Dempsey was nominated as his replacement.
According to the Pentagon, Mr. Lynn was in charge of Pentagon strategy and budgets and helped develop “a landmark cyber strategy to protect the nation in the digital age, including the creation of the U.S. Cyber Command.”
Mr. Lynn’s appointment generated controversy in 2009 as a result of his past position as a lobbyist for Raytheon, a defense contractor. Mr. Lynn received a waiver from the Obama administration’s ban on lobbyists in public positions.
Mr. Panetta’s office said the search for a replacement deputy secretary is under way.
Among the likely candidates mentioned as replacements are Ashton Carter, undersecretary of defense for acquisition; Michele Flournoy, undersecretary of defense for policy; and retired Army Gen. Eric Shinseki, currently secretary of veterans affairs.
Mr. Obama announced earlier this year that he plans to cut $400 billion from Pentagon spending over the next decade.
The cuts come at a time of fiscal constraint and when the U.S. military needs to replace equipment and upgrade weapons.
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