By Marina Malenic

President-elect Barack Obama’s transition team announced yesterday that he plans to nominate William Lynn to be the new Deputy Secretary of Defense.

Lynn served as the Pentagon comptroller from 1997 to 2001. From 1993 to 1997, Lynn was the director of program analysis and evaluation in the Office of the Secretary of Defense, where he oversaw all aspects of the DoD’s strategic planning process. He currently serves as senior vice president of Government Operations and Strategy at Raytheon [RTN].

Lynn’s selection appears to have support on Capitol Hill.

House Appropriations Defense subcommittee Chairman John Murtha (D-Pa.) told reporters this week Lynn is a good pick because of his managerial experience in the Pentagon, and that an administrator is needed in the position.

Murtha and other lawmakers had criticized an arrangement, rumored previously, for former Navy Secretary Richard Danzig to serve as Gates’s deputy before eventually replacing Gates. They charged it would undermine Gates to have his successor-in-waiting working directly under him.

Senate Armed Services Committee member Sen. Jack Reed (D-R.I.), who also called for a managerially focused deputy defense secretary, praised Obama’s Pentagon picks yesterday.

“Bill Lynn is a distinguished public servant and a real expert on national security issues,” Reed said in a statement. “He knows the intricacies of the Pentagon and is superbly prepared for this job. Along with Michele Flournoy and the other appointees, President-elect Obama has selected strong leaders who have shown strategic vision and pragmatism.”

According to sources, Harvard Professor Ashton Carter has emerged as the leading contender for Pentagon acquisition chief. Carter, who has spent his entire career in academia and government, served as Assistant Secretary of Defense for International Security Policy in the Clinton administration.

Obama’s team also announced his intention to appoint Robert Hale to be the new Pentagon comptroller, Michele Flournoy as the undersecretary for policy and Jeh Charles Johnson as general counsel.

“Together with Secretary [Robert] Gates and our military, we will work to responsibly end the war in Iraq, defeat al Qaeda and the Taliban, and renew America’s strength and standing in the world,” Obama said in a statement released via email. “I am honored that they have joined me in this mission, and I trust that they will serve the American people well.”

Hale currently serves as the Executive Director of the American Society of Military Comptrollers. From 1994 to 2001, he served as the Air Force comptroller. Flournoy is president of the Center for a New American Security, a centrist national security think tank in Washington, and Johnson is a partner in the law firm of Paul, Weiss, Rifkind, Wharton & Garrison LLP, based in New York City.