By Byron Tau And Peter Nicholas 

The State Department had no permanent inspector general--the lead watchdog charged with uncovering misconduct and waste--during Hillary Clinton's entire tenure as secretary, leaving in place an acting inspector who had close ties to State Department leadership.

President Barack Obama didn't put forward a nominee to lead the inspector general's office while Mrs. Clinton led the State Department, making it the only agency with a presidentially appointed inspector general that had neither a confirmed nor nominated head watchdog during that full time period.

Five months after Mrs. Clinton left office, Mr. Obama nominated a permanent inspector general, who was confirmed by the Senate three months later.

The lack of a confirmed inspector general raises questions about oversight of the department under Mr. Obama and Mrs. Clinton. The department has been criticized for its failure to gather and archive the email records of Mrs. Clinton and other officials and for responses to public-record requests that lawmakers and advocacy groups say were insufficient, including its response to requests for information from a congressional panel investigating the 2012 terror attack in Benghazi, Libya.

The vacancy in the top watchdog spot left the State Department with no confirmed inspector general for more than five years, the longest gap since the position was created in 1957, according to department records. While other agencies have had no permanent inspectors general at various points in recent years, some of those vacancies were due to a lack of confirmation by the Senate on nominees put forward by Mr. Obama.

Is isn't clear whether Mrs. Clinton had any role in the lack of a nomination.

The acting inspector general, Harold Geisel, had served in a variety of roles, including U.S. ambassador to Mauritius in Bill Clinton's administration and in a State Department job under Richard Nixon. Because he was a longtime foreign-service officer, Mr. Geisel was banned by law from becoming permanent inspector general, a prohibition that Congress put in place to ensure that oversight is conducted by people who don't have ties to the departments they investigate.

"It's a convenient way to prevent oversight," said Matthew Harris, a University of Maryland University College professor who has worked in law enforcement and researches inspectors general. Acting inspectors general "don't feel empowered; they don't have the backing of their people. They're in a position where they could be removed at any moment, " Mr. Harris said.

Rep. Ed Royce (R., Calif.), chairman of the House Foreign Affairs Committee, said Mr. Geisel's role as a Clinton administration ambassador undercut his status as a watchdog.

"We did not believe he could be truly independent. We raised the issue that the lack of a permanent IG was a problem," Mr. Royce said. He said an independent inspector would likely have uncovered and raised objections to Mrs. Clinton's use of a private email account and computer server for official correspondence.

"A permanent IG would have objected to her efforts to circumvent congressional oversight by keeping her emails off the books," Mr. Royce said.

A spokesman for Mrs. Clinton, Nick Merrill, said Mr. Geisel "was a career official spanning Republican and Democratic administrations alike, independent and hard-hitting. As it should be." A spokesman for the State Department said Mr. Geisel led a team that "conducted more investigations between 2007 and 2012 than the IG had under his predecessor."

The White House declined to elaborate on reason for the lack of an appointment. A White House spokesman said the inspector general's office issued more than 450 reports while there was no permanent head in place.

Mr. Geisel, assuming his tenure would be short-lived, said he did little to decorate his office. "I never even put up a picture," he said in an interview. After his five-year stint as watchdog, the State Department gave him a paid temporary assignment reviewing staffing conditions at outposts in Egypt and Nairobi, Mr. Geisel said.

Designed to be isolated from political pressure, inspectors general are tasked with uncovering waste, fraud, abuse and mismanagement of federal agencies. The State Department office has a large staff that conducts audits and investigations.

During Mr. Geisel's tenure, members of Congress and independent watchdog groups raised questions about his distance from top leadership at the State Department.

The nonpartisan Project On Government Oversight said Mr. Geisel had an unduly close relationship with Patrick F. Kennedy, the department's undersecretary for management, a top post. In a 2010 letter to the White House, the group cited friendly emails between the two as evidence of a close relationship, as well as the fact that Mr. Geisel recused himself from an investigation into a situation involving Mr. Kennedy at one point during his tenure.

Asked whether he believed he was compromised in his ability to do his job, Mr. Geisel said: "My work absolutely speaks for itself." He described his mission as "telling the truth that needs to be told, which may not be the truth that people want to hear."

One person who worked in the office from 2009 to 2013, Evelyn Klemstine, spoke highly of Mr. Geisel. "I personally never felt that he inhibited any of the audits that we did," she said.

Write to Peter Nicholas at peter.nicholas@wsj.com

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