William Lynn III, the top lobbyist for Raytheon Co., was chosen by Obama and Defense Secretary Robert M. Gates for the position of deputy secretary of Defense.
The new ethics rules banned lobbyists from serving in the administration. But the executive order allowed waivers to let some former lobbyists take government jobs if doing so was in the public interest.
On Thursday, Sen. Carl Levin (D-Mich.), chairman of the armed services committee, said he would need further information on the White House waiver for Lynn before considering his nomination.
Levin said he was worried that if Lynn had to recuse himself from any issue that could affect Raytheon, he would be unable to do his job effectively. The Pentagon deputy typically runs much of the day-to-day operation of the Defense Department and handles many key budget and procurement decisions.
Raytheon, one of the five largest U.S. defense contractors, is a key supplier of missiles and radar to the military. The Waltham, Mass.-based company also produces components of the missile defense system.
If confirmed for his position, Lynn probably would have a large say in the future of the missile defense system. If the Obama administration decided to scale that program back dramatically, for instance, it would affect Raytheon.
Gates pushed hard for Lynn's appointment and favored him over other officials suggested by the Obama transition team. At a news conference Thursday, Gates said he was impressed with Lynn and argued he should get the job despite the lobbying ban.
"I asked that an exception be made because I felt that he could play the role of the deputy in a better manner than anybody else that I saw," Gates said.
White House officials said they had provided Levin with the language of the waiver and assured the Senate committee that Lynn would not be prevented from doing his job by recusing himself from issues involving Raytheon.
The White House has also issued a waiver for William V. Corr, a former lobbyist for the anti-smoking group Campaign for Tobacco-Free Kids, who has been nominated for a top position at the Department of Health and Human Services.
"Even the toughest rules require reasonable exceptions," White House Press Secretary Robert Gibbs said in a statement. "Our waiver provisions are designed to allow uniquely qualified individuals like Bill Corr and Bill Lynn to serve the public interest in these critical times."
But a government watchdog group raised questions about Lynn's appointment and urged the Obama administration to choose someone else.
"The guy is either in violation of this executive order, which we approve of, or the guy can't do his job," said Danielle Brian, executive director of the Project on Government Oversight. "If he recuses himself from anything to do with Raytheon, he can't be the No. 2 at the Pentagon."
Brian said the group, which focuses much of its work on Pentagon spending abuses, said the lobbying rules would curb abuses associated with the revolving door between government and industry. But she said that a top official, especially a lobbyist, from a defense contractor should not be chosen for the second-highest Pentagon post.
"Why be concerned about the revolving door at all?" Brian said. "While people are serving [in government], they shouldn't have dual loyalties."