William J. Lynn III

Despite delays and lingering questions over his lobbying history, William J. Lynn, the nominee for the No. 2 spot at the Pentagon, was confirmed by the Senate today, a victory for the Obama administration.

Obama's choice of Lynn, a former Pentagon official under President Bill Clinton and Obama's choice for deputy defense secretary, had come under fire for being in breach of the new administration's ethics rule barring ex-lobbyists from working on issues they have lobbied about in the past two years.

Lynn spent the better part of the past two years lobbying for defense contractor Raytheon. But he received a special waiver from the president to take office.

Lynn noted that he personally lobbied members of Congress and their staffs on only a "handful of programs," and only lobbied the Defense of Department on one program, the Multiple Kill Vehicle.

Raytheon was awarded a $54 million Missile Defense Agency contract in November to continue the design and development of the hovering military vehicle.

Lynn was thought to have "broad support in Congress" and had been considered a "shoo-in," according to The Associated Press.

But watchdog groups, the Republican National Committee and Sen. John McCain (R-Ariz.) had expressed their reservations. Despite the cool reception, the Senate Armed Services Committee voted to support Lynn's nomination a week ago followed by today's 93-4 vote in the Senate.