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WASHINGTON — President-elect Barack Obama appointed a Raytheon Co. lobbyist Thursday to become the No. 2 official at the Defense Department, acknowledging that his choice appeared to break with his self-imposed rules to keep lobbyists at arm's length.

William J. Lynn III, Obama's choice for deputy defense secretary, is a former Pentagon official who now is senior vice president for government operations at Raytheon Co. Lynn hasn't been a registered lobbyist since July, meaning he can't personally lobby Congress or the White House. In the first three months of 2008, his lobbying team reported spending $1.15 million to influence issues, including missiles, sensors and radar, advanced-technology programs and intelligence funding.

Obama has vowed that no political appointees in his administration would be permitted to work on areas that "directly and substantially related to their prior employer for two years." His transition team, which voluntarily disclosed Lynn's lobbying activities, said Lynn's talents made him worth the apparent exception to the spirit of Obama's anti-lobbyists policy. It said it will work with Lynn to maintain Obama's high ethics standards.

"Because Mr. Lynn came so highly recommended from experts across the political spectrum, the president-elect felt it was critical that he fill this position," Obama spokesman Tommy Vietor said.

Some government watchdogs questioned the revolving-door aspect of Lynn's appointment even while acknowledging his qualifications.

"He left public service and went into lobbying for one of the largest defense contractors in the nation. And that's the part that's troubling," said Bill Buzenberg, executive director of the Center for Public Integrity. "Even if he's completely aboveboard and ethical, it raises questions about his loyalty."

During his presidential campaign, Obama took pains to tell voters he wouldn't tolerate influence-peddling. "I am in this race to tell the corporate lobbyists that their days of setting the agenda in Washington are over," Obama said in November 2007 in Des Moines, Iowa.

It will be difficult for Lynn to avoid defense issues related to Raytheon, said James Thurber, who teaches lobbying at American University.

"I think it's impossible in our system not to have people that have been in the advocacy system," he said. "They're the people who know the issues and have the expertise." The key is for the administration to disclose those connections and avoid financial conflicts, he said.

Under Obama's rules, political appointees also would be precluded from lobbying the executive branch after leaving government service during the remainder of the administration.

If confirmed by the Senate, Lynn would become the top civilian assistant to Defense Secretary Robert Gates.

Lynn has been an officer with Raytheon, based in Waltham, Mass., since 2005. He was at the Pentagon from 1993 to 2001 as undersecretary in charge of the budget and oversaw strategic planning. He earlier worked for Sen. Edward Kennedy, D-Mass.