updated 1/8/2009 5:21:51 PM ET 2009-01-08T22:21:51

President-elect Barack Obama appointed a defense contractor's executive 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.

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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 involving 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.

Vietor declined to comment further on whether Lynn would have to remove himself from involvement on any issues.

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 above board 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. "I have done more than any other candidate in this race to take on lobbyists and won. They have not funded my campaign, they will not run my White House, and they will not drown out the voices of the American people when I am president."

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, who is staying on in the top civilian job.

Lynn served 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.

Lynn has been an officer with Waltham, Massachusetts-based Raytheon since 2005.

The company, with 2007 sales of $21.3 billion, specializes in worldwide defense and homeland security-related sales.

Obama's transition office announced the names of several other Pentagon selections on Thursday, including Michele Flournoy for the No. 3 job as policy chief. Also a Clinton-era aide at the Pentagon, Flournoy has been the co-chair of Obama's Pentagon transition team.

In a statement, Obama said he is confident his picks will help build what he called a sustainable national security strategy that answers the threats of the 21st century.

Pentagon spokesman Geoff Morrell said Gates welcomes the selections and hopes for a quick confirmation. "Prompt hearings and confirmation will help ensure a smooth transition of power in the Pentagon as we continue to fight wars in Iraq and Afghanistan," he said.

Sen. Jack Reed, a member of the Senate Armed Services Committee, said Obama's picks were "strong leaders who have shown strategic vision and pragmatism."

Reed said Lynn in particular brought "a great deal of wisdom and experience to the table."

Copyright 2008 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

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