President Obama's top Pentagon nominee hit an unexpected bump in the road to confirmation Thursday, after officials said he would need a waiver from the administration's strict new ethics rules.

William J. Lynn III, the president's pick to be deputy to Bush holdover Defense Secretary Robert Gates, is a lobbyist for giant arms contractor Raytheon -- which normally would prohibit him, under Obama's first-ever executive order Wednesday, from taking a job in the government for two years.

Lynn, who was in charge of the Pentagon's notoriously chaotic finances under President Bill Clinton, was "uniquely qualified" to do the job, Obama spokesman Robert Gibbs told reporters, and would be issued one of "a very limited number of waivers" from the new rules.

"Even the toughest rules require reasonable exceptions," said Gibbs.

Gates told a briefing at the Pentagon that the issue of Lynn's work as a lobbyist had been flagged up early in the process of choosing a deputy.

"People in the transition certainly recognized that it was an issue," he said, adding, "I was very impressed with his credentials. ... And I asked that an exception be made (to the ban on lobbyists serving in the administration), because I felt that he could play the role ... of deputy in a better manner than anybody else that I saw."

But the news meant his nomination would be delayed, said Senate Armed Services Committee Chairman Carl Levin, D-Mich.

The committee "will need further information before proceeding with the nomination," said Levin in a statement, adding the committee would "await the administration's assessment as to … whether a waiver will be forthcoming and what the scope of the waiver will be."

Government ethics watchdogs said they were disappointed. "It takes most of the air out of (Obama's) announcements ... if you are going to riddle them with waivers and recusal statements," said Scott Amey, general counsel of the non-profit Project on Government Oversight.

The group called for Lynn's nomination to be withdrawn. "If (Obama) wants his message (on ending the revolving door between lobbying and government) to be clear … there are other people he can turn to," said Amey.

Administration officials nonetheless appeared confident Lynn's nomination would proceed, saying they were working with Levin's staff to get them the information he wanted.

"He supports the nomination," one told UPI of Levin. "It will go forward."

Even Sen. Claire McCaskill, D-Mo., who questioned Lynn closely at his confirmation hearing about his role as a lobbyist and the revolving door, said through a spokeswoman that she would not oppose the nomination.

"The way (the Department of Defense) does business with defense contractors must change, because the status quo is unacceptable," said McCaskill in a statement for the record on the Senate floor Wednesday. "In part because of Mr. Lynn's recent past" working for Raytheon, the fourth-largest U.S. defense contractor, "I am concerned that he will not bring the sense of urgency to, or worse yet, see the need for substantial reform in (the Department of Defense's) weapons and services procurement practices."

McCaskill went on to say that she had "not sensed a strong commitment to this type of change" from him and that she had "significant concerns about the message (his) nomination and confirmation … will send within the Department of Defense and across the federal government."

But McCaskill spokeswoman Maria Speiser told UPI the senator would not oppose the Lynn nomination. "She is giving him the benefit of the doubt," she said. "He is giving up a lot to come back to public service, and the senator appreciates that."

But Speiser added McCaskill "will be watching closely. … She was very tough on the Bush administration on these issues, and she plans to be just as tough on the new administration."

Wednesday's executive order on administration ethics states that White House Office of Management and Budget Director Peter Orszag may issue waivers of the rules for current or former officials if he certifies in writing that it is in the public interest to do so.

"The public interest shall include, but not be limited to, exigent circumstances relating to national security or to the economy," states the order.

Officials were not able to say how long the process of certifying and signing the waiver would take.