Lynn, for whom the White House had to waive tough new ethics rules, will also require special permission from Pentagon ethics officials to make decisions about other defense programs that might affect his former employer.
In letters to Sen. John McCain of Arizona, the senior Republican on the Senate Armed Services Committee, Lynn last month sought to allay concerns that his work for Raytheon would affect his ability to do his new job. He cited the special permission requirement -- known as a Section 502 process -- and voluntarily recused himself from six major programs that he had personally lobbied Congress or the Pentagon on: including the Multiple Kill Vehicle, part of the controversial Ballistic Missile Defense System; the huge but now-defunct U.S. Air Force Future Imagery Architecture satellite; and the Navy's troubled DDG-1000 destroyer.
Lynn's defenders argue that he is the best man for the job and that the well-established ethics process, which will have to be invoked for decisions about the hundreds of Pentagon programs involving his former employer, will be manageable.
But the forest of ethics restrictions that will hedge around his decision-making authority is already leading some to question whether he will be able to effectively do his job.
"Absolutely, it will make his job harder," Thomas Christie, who was the Pentagon's director of operational testing from 2001 to 2005, told United Press International. "The deputy secretary is, for the most part, the guy who runs the building and makes the decisions" on big-ticket acquisition programs. "If he has to recuse himself (from such decisions), it will place a burden on the process. … It sounds awfully onerous to me."
Christie, a Pentagon veteran who has worked on acquisition issues for 20 years, pointed out that the Section 502 process would need to be invoked for decisions about potentially hundreds of programs in which Lynn's former employer was involved.
"Raytheon is involved in so many programs," he said of the Waltham, Mass.-based company, one of the top five defense contractors in the country.
Christie said that decisions Lynn could not take for ethical reasons would likely be "kicked upstairs" to Defense Secretary Robert Gates. "I don't see how you can push these decisions (further) down" the Pentagon chain of command, he said. "Gates is going to get dragged into these decisions," he added, noting that as well as adding to the secretary's workload, "You run the risk that he (Gates) will not be up to speed on the issues.
"It could become a bureaucratic nightmare," Christie concluded.
Sen. Charles Grassley, R-Iowa, wrote earlier this month to White House Office of Management and Budget Director Peter Orszag, the man who issued Lynn's waiver from the administration's ban on lobbyists serving in the government.
The "recusal requirements could limit Mr. Lynn's effectiveness as deputy secretary," the letter says.
Lynn, if confirmed, "would be the final approval authority on most -- if not all -- contract, program and budget decisions. Surely, a number of Raytheon issues would come across his desk," Grassley wrote. He concluded that Lynn's role would create an "impossible" conflict of interest.
Pentagon spokesman Geoff Morrell said the administration was confident about Lynn's role. "Obviously, given the demands of the job, we would prefer to have the deputy secretary be able to tackle all the issues that come before that office, but even with the restrictions Mr. Lynn has agreed to, we are confident he will be a vital and effective member of Secretary Gates' leadership team," Morrell told UPI in an e-mail message.
That confidence was echoed by Stan Soloway, president and CEO of the Professional Services Council, a trade association that represents government contractors. Lynn's situation would be "very manageable," he said.
Soloway, who served with Lynn during the latter's last stint at the Defense Department in the Clinton administration, praised his qualities. "There's an openness there," he said of Lynn, an "innate sense of public service and integrity."
"Just because someone has had to register as a lobbyist does not mean they can't be fair and objective," he said, adding he had heard no disquiet among Raytheon's competitors about the nomination. "If anything," he said, "the greatest discomfort is probably at Raytheon, because of a perception he may have to bend over backwards" to be sure of being seen not to be favoring the company.
"I have great confidence in Bill," he concluded.
But Christie said Lynn's situation would be especially severely impacted because important decisions on some "big and controversial" programs were overdue, having been "kicked down the road" by the outgoing administration.
Ballistic missile defense and the DDG-1000 program were both "big things they will have to make decisions on in this budget cycle," he said.
As chairman of the Defense Resources Board, the deputy secretary is supposed to helm the process of examining where such multibillion-dollar acquisition and procurement programs fit into the department's overall priorities.
Even when more junior people in the decision-making process had to recuse themselves from decisions -- as Pentagon acquisition chief John Betti had to in the 1980s -- Christie said the consequences were severe: "It was a nightmare."
Soloway said that concern over Lynn's situation reflected the possibility that the pendulum on government ethics had swung too far.
"This is an example of a well-intentioned policy … of why you can't be too absolute about these matters," he said. "Lobbying is not inherently evil."
The ethics rules, including the Section 502 process and the administration's new ban on lobbyists, were "a system designed to protect against the very, very small proportion of people who might try to do wrong," Soloway said, and care was needed to ensure that the unintended negative consequences did not outweigh the benefits.
"Pendulums are always swinging in this town," he said, adding that we live "in an era where there's a major effort to restore public confidence in government."