NCIX chief of staff Robert L. Hubbard also was reassigned to another post in the aftermath of the IG review, officials said. Mr. Hubbard declined to comment through an agency spokesman.

The agency's chief, National Counterintelligence Executive Joel F. Brenner, told The Times that neither official was dismissed but that it was his decision to prompt the moves. "I felt it was time to make a change in NCIX management," he said, declining to be more specific because of personnel privacy issues.

Rep. Peter Hoekstra of Michigan, the ranking Republican on the House Permanent Select Committee on Intelligence, said the committee was informed that the IG probe had uncovered problems and recommended some management changes inside NCIX.

"We're going back to take a second look at this as part of our oversight responsibilities," Mr. Hoekstra said.

Mr. Bowman had been granted a waiver from federal rules to return from his retirement from the Navy and FBI and work for NCIX under contract, officials familiar with the arrangement said. The officials said a decision was made not to renew his contract after the IG issued an eight-page management review of the office. The review raised issues involving management capabilities but did not purport any misconduct or abuses, the officials said.

Mr. Bowman said in an interview that he had planned to leave the agency for months but his departure ultimately was prompted by "ethical issues" uncovered during the IG inquiry. He declined to elaborate. He said his background was mainly working as an intelligence operator and that Mr. Brenner needed a deputy who was a better administrator.

NCIX is a little-known agency that was created under a December 2000 presidential directive in the aftermath of the CIA's Aldrich Ames spy case. After the FBI's Robert P. Hanssen spy case in 2001, the office was given greater stature under 2002 law aimed at improving counterspy efforts.

The office is staffed by people from other intelligence agencies. It conducts damage assessments of spy cases and helps coordinate counterintelligence policies.

However, the agency and its leaders cannot direct anti-spying operations or budgets, which are controlled mainly by the major counterintelligence agencies, the FBI domestically and the CIA abroad.

Mr. Brenner took over the agency in 2006 and removed most of the staff who had worked under the previous director, Michelle Van Cleave, former NCIX officials said.

NCIX was made one of three major "centers" when the office of the Director of National Intelligence was created by a 2004 law.

Miss Van Cleave recently published an article stating that NCIX and other U.S. efforts to counter foreign spies remain ineffective while the problem of foreign spying is growing.

Miss Van Cleave, writing in The Washington Post on Feb. 8, identified concerns about U.S. counterintelligence while she was at NCIX for three years during the Bush administration. The article noted problems that she outlined in a report made public in September by the Project on National Security Reform, a private research group.

"I am hopeful that the new DNI will give counterintelligence the priority attention it deserves," Miss Van Cleave told The Washington Times. "As a former four-star combatant commander, Admiral Dennis Blair [the new director of national intelligence] well understands the value of strategic clarity, which is what the NCIX job is all about."

Despite the damaging spy cases, U.S. intelligence agencies have "no coherent game plan" for identifying and stopping foreign spy activities, she stated in the article in The Post.

Miss Van Cleave also said U.S. counterintelligence agencies failed to find out how Chinese spies obtained U.S. nuclear weapons secrets. "The Chinese stole the design secrets to all - repeat, all - U.S. nuclear weapons, enabling them to leapfrog generations of technology development and put our nuclear arsenal, the country's last line of defense, at risk," she said. "To this day, we don't know quite when or how they did it, but we do know that Chinese intelligence operatives are still at work, systematically targeting not only America's defense secrets but our industries' valuable proprietary information."

Mr. Brenner declined to comment on the criticism. He said he has no plans to leave the counterspy position as the result of the arrival of Mr. Blair under the new administration of President Obama.

Mr. Bowman spent 11 years as the national security general counsel at the FBI and was involved in the prosecutions of Soviet spy John A. Walker Jr., who passed naval codes, and Israeli spy Jonathan Pollard, a naval intelligence analyst, as an attorney for the Office of Naval Intelligence.

Mr. Bowman recently signed a Supreme Court brief opposing the holding of Ali Saleh al Marri, an al Qaeda suspect arrested in Illinois in 2001 who has been held without being charged in a military brig in South Carolina as an enemy combatant. Mr. Bowman told the Daily News that "coercive interrogations don't work and fall outside the legal and moral obligations that this nation assumed in 1776."

Mr. Bowman, a retired Navy captain, also has opposed detainee abuses at Guantanamo Bay prison, which Mr. Obama recently ordered closed.

Senate Judiciary Committee members criticized Mr. Bowman several years ago for his failure to authorize counterterrorist surveillance in the case of Zacarias Moussaoui, a suspected al Qaeda terrorist who was detected by the FBI taking flight lessons in Minnesota and who some officials suspect was supposed to have been one of the Sept. 11 hijackers but was arrested before he could take part.

Sen. Charles E. Grassley, Iowa Republican, said in a statement that he has heard conflicting reports on why Mr. Bowman and Mr. Hubbard left the NCIX. "This isn't the first time Mr. Bowman has been at the center of controversy, so I hope the Inspector General will provide its report to Congress so that we can determine whether it contains any cause for concern about potential misconduct," Mr. Grassley said.

The senator stated in a 2003 letter to FBI Director Robert S. Mueller III that giving Mr. Bowman the Presidential Rank Award sent the wrong message to the FBI because of problems related to the FBI's mishandling of Foreign Intelligence Surveillance Act requests. The FBI's FISA problems "are not Mr. Bowman's fault, but many of them have occurred during Mr. Bowman's tenure," Mr. Grassley stated.