WASHINGTON, Oct. 11 — The director of the Central Intelligence Agency, Gen. Michael V. Hayden, has ordered an unusual internal inquiry into the work of the agency’s inspector general, whose aggressive investigations of the C.I.A.’s detention and interrogation programs and other matters have created resentment among agency operatives.
A small team working for General Hayden is looking into the conduct of the agency’s watchdog office, which is led by Inspector General John L. Helgerson. Current and former government officials said the review had caused anxiety and anger in Mr. Helgerson’s office and aroused concern on Capitol Hill that it posed a conflict of interest.
The review is particularly focused on complaints that Mr. Helgerson’s office has not acted as a fair and impartial judge of agency operations but instead has begun a crusade against those who have participated in controversial detention programs.
Any move by the agency’s director to examine the work of the inspector general would be unusual, if not unprecedented, and would threaten to undermine the independence of the office, some current and former officials say.
Frederick P. Hitz, who served as C.I.A. inspector general from 1990 to 1998, said he had no first-hand information about current conflicts inside the agency. But Mr. Hitz said any move by the agency’s director to examine the work of the inspector general would “not be proper.”
“I think it’s a terrible idea,” said Mr. Hitz, who now teaches at the University of Virginia. “Under the statute, the inspector general has the right to investigate the director. How can you do that and have the director turn around and investigate the I.G.?”
A C.I.A. spokesman strongly defended the inquiry on Thursday, saying General Hayden supported the work of the inspector general’s office and had “accepted the vast majority of its findings.”
“His only goal is to help this office, like any office at the agency, do its vital work even better,” said Paul Gimigliano, the spokesman.
Current and former intelligence officials said the inquiry had involved formal interviews with at least some of the inspector general’s staff and was perceived by some agency employees as an “investigation,” a label Mr. Gimigliano rejected.
Several current and former officials interviewed for this article spoke on condition of anonymity because of the sensitivity of the inquiry.
The officials said the inquiry was being overseen by Robert L. Deitz, a trusted aide to the C.I.A. director and a lawyer who served as general counsel at the National Security Agency when General Hayden ran it. Michael Morrell, the agency’s associate deputy director, is another member of the group, officials said.
Reached by phone Thursday, both Mr. Helgerson and Mr. Dietz declined to comment.
In his role as the agency’s inspector general since 2002, Mr. Helgerson has investigated some of the most controversial programs the C.I.A. has begun since the Sept. 11 attacks, including its secret program to detain and interrogate high value terrorist suspects.
Under federal procedures, agency heads who are unhappy with the conduct of their inspectors general have at least two places to file complaints. One is the Integrity Committee of the President’s Council on Integrity and Efficiency, which oversees all the inspectors general. The aggrieved agency head can also go directly to the White House.
If serious accusations against an inspector general are sustained by evidence, the president can dismiss him.
Both those routes avoid the awkward situation officials describe at the C.I.A. and preserve the independence of the inspector general.
But one intelligence official who supports General Hayden’s decision to begin an internal inquiry said that going outside the agency would “blow things way out of proportion.”
A report by Mr. Helgerson’s office completed in the spring of 2004 warned that some C.I.A.-approved interrogation procedures appeared to constitute cruel, inhuman and degrading treatment, as defined by the international Convention Against Torture.
Some of the inspector general’s work on detention issues was conducted by Mary O. McCarthy, who was fired from the agency last year after being accused of leaking classified information. Officials said Mr. Helgerson’s office was nearing completion on a number of inquiries into C.I.A. detention, interrogation, and “renditions” — the practice of seizing suspects and delivering them to the authorities in other nations.
The inspector general’s office also rankled agency officials when it completed a withering report about the C.I.A’s missteps before the Sept. 11 attack — a report that recommended “accountability boards” to consider disciplinary action against a handful of senior officials.
When the report was made public in August, General Hayden took the rare step of pointing up criticisms of the report by the former intelligence director, George J. Tenet and his senior aides, saying many officials “took strong exception to its focus, methodology and conclusions.”
Some agency officers believe the aggressive investigations by Mr. Helgerson amount to unfair second guessing of intelligence officers who are often risking their lives in the field.
“These are good people who thought they were doing the right thing,” said one former agency official. “And now they are getting beat up pretty bad and they have to go out an hire a lawyer.”
Agency officials have also criticized the length of the inspector general’s investigations, some lasting more than five years, which have derailed careers and generated steep legal bills for officers under scrutiny.
The former agency official called General Hayden’s review of the inspector general “a smart move.”
Since taking over at the C.I.A. in 2006, General Hayden has taken several steps to soothe anger within the agency’s clandestine service, which has been buffeted in recent years by a string of prolonged investigations.
He has brought back two veteran agency operatives, Steven R. Kappes and Michael J. Sulick, both of whom angrily left during the tenure of Porter J. Goss, the C.I.A. director, to assume top posts at the spy agency. He also supported the president’s nomination of John A. Rizzo, a career agency lawyer and someone well-respected by covert operatives, to become the C.I.A’s general counsel.
Mr. Rizzo withdrew his nomination to the post last month in the midst of intense opposition from Senate Democrats.
“Director Hayden has done a lot of things to convince the operators that he’s looking out for them, and putting the I.G. back in its place is part of this,” said John Radsan, who worked as a C.I.A. lawyer from 2002 to 2004 and is now a professor at William Mitchell College of Law.
Mr. Hitz and other former C.I.A. officials said tensions between the inspector general and the rest of the agency were natural. Conflicts most often arise when the inspector general reviews the actions of the agency’s directorate of operations, now known as the National Clandestine Service, which recruits agents and hunts terrorists overseas.
“The perception is like in a police department between street cops and internal affairs,” said A. B. Krongard, the agency’s executive director from 2001 to 2004.
Resentment of the inspector general’s work has also at times extended to the agency’s general counsel’s office, whose legal judgment is sometimes second-guessed by after-the-fact investigations. “In some of our reports, we were quite critical of the advice given by the general counsel,” Mr. Hitz said.
The C.I.A., created in 1947, had an in-house inspector general selected by the director starting in 1952 who investigated failed operations like the Bay of Pigs invasion against Cuba in 1961.
But that position was viewed as lacking clout and independence, and in 1989, partly in response to the Iran-contra affair, Congress created an independent inspector general at the agency, appointed by the president and reporting to both the director and to Congress.
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