State Department Inspector General officials edited out passages of a high-profile report in 2013 that could have embarrassed Hillary Clinton just days before she quit President Obama's Cabinet.

The officials excised details of a cover up of misconduct by Clinton's security team.

The edits raise concerns that investigators were subjected to "undue influence" from agency officials.

The Washington Examiner obtained earlier drafts of the report which differ markedly from the final version. References to specific cases in which high-level State officials intervened and descriptions of the extent and frequency of those interventions appear in several early drafts but were later eliminated.

The unexplained gaps in the final version, and the removal of passages that would have damaged the State Department, call into question the independence of Harold Geisel, who was State's temporary inspector general throughout Clinton's four years at the head of the department.

The drafts were provided to the Examiner by Richard Higbie, a senior criminal investigator at the Bureau of Diplomatic Security, after he said he disclosed the documents to several members of Congress and multiple congressional committees under federal whistleblower protections.

Higbie is presently suing the State Department for retaliation.

The Bureau of Diplomatic Security's special investigations unit "lacks a firewall to preclude the [diplomatic security] and Department of State hierarchies from exercising undue influence in particular cases," the published version stated.

The same final version mentions only that "the perception exists among knowledgeable parties that external influences have negatively affected some [special investigations division] investigations."

But an earlier version dated November 16, 2012, reveals much greater detail about internal investigations that were blocked by top State Department officials.

"Inspectors learned in conversations with Department employees…that in some cases superiors in [diplomatic security] and in senior levels of the State Department have prejudiced the commencement, course and outcome of [special investigations division] investigations," the early draft said.

"Sources referred to [diplomatic security] sometimes circling the wagons to protect favored [diplomatic security] rising stars from criminal charges or from embarrassing revelations that could harm a promising career," the draft continued.

"One case, which triggered outraged comment from several [special investigations division] sources, relates to allegations that a Regional Security Officer engaged in serious criminal conduct including sexual abuse of local embassy staff during a series of embassy postings. Sources also reported that a senior [diplomatic security] official successfully protected some agents on the Secretary's Detail from investigations into misbehavior while on official trips," the November 16 draft said.

It is unclear why this critical text was stripped from the report before the inspector general published it in February 2013.

Another passage that was removed from the public report suggests officials in Clinton's office may have protected an ambassador from a child abuse investigation.

"Sources reported that a senior '7th Floor' Department official ordered [diplomatic security] to stop the investigation of an ambassador accused of pedophilia, and another such senior official had [diplomatic security] stop an investigation of an ambassador-designate," the draft reads.

The seventh floor is the location of the secretary of state's office, as well as the offices of the deputy secretary and the undersecretaries, according to the State Department's website. If any of these details were removed because of exculpatory information, this is never stated.

The same section of the final report, titled "Need for Independence," makes no reference to the pedophilia allegations or the sexual abuse charges that were covered up by State Department staff.

A subsequent passage that is completely redacted in the published document, but is revealed in the November 16 draft, shows investigators were concerned about their physical proximity to the subjects of their investigations at the agency.

Many of the bureau of diplomatic security officials whom the investigators probed "often return to work" with firearms in tow.

Some investigators "pointedly carry their own firearms constantly" while in the State Department office because they are afraid of "a nasty elevator confrontation."

The inspector general recommended moving the special investigations division to another office to avoid "the threat of violent confrontations." All of those warnings were redacted from the public report.

Geisel's years as acting inspector general have come under fire in recent weeks as scrutiny has grown over Clinton's use of a private email and server to keep her communications out of the public record.

Geisel served as the State Department's interim inspector general from January 2008-June 2013.

Lawmakers have questioned why the agency's watchdog position was left empty for more than five years, creating what was then the longest such vacancy in the history of any federal agency.

Rep. Ed Royce, R-Calif., chairman of the House Foreign Affairs Committee, demanded the inspector general turn over earlier drafts of the published report in question in June 2013 after media reports suggested it had been softened internally before its release.

Royce said in the letter to Geisel that the inspector general's office had turned over to Congress two drafts of the report — one dated November 20, 2012, and another from December 4, 2012.

But an Examiner review of the documents indicates there are several additional drafts of the report that were not initially submitted to the committee upon request, according to Royce's first letter.

Hand-written comments in the margin of a November 27, 2012, draft of the report suggest there was an internal struggle over what information should be included in the document.

Next to the passage describing an investigation into the pedophilia allegations against an unnamed ambassador, for example, someone typed: "[T]hese allegations must be deleted." Someone else wrote, "Why?" in the space below.

While the question wasn't answered in a nearly identical draft that followed on November 28, the offending language was missing from a December 4, 2012, version of the report.

Citizens United, a conservative nonprofit, filed a Freedom of Information Act request seeking records related to the February 2013 report in September of last year.

After the group sued the State Department over their stonewalled request, agency officials claimed there were simply too many responsive documents to provide even an estimate of how many records might have mentioned the interim inspector general or the report in question.

The inspector general's office refused to comment on the earlier drafts of the report and said the final, published document should speak for itself.

Allegations that high-level State Department officials had stymied diplomatic security investigations first surfaced in 2013 when Aurelia Fedenisn, a former investigator in the State Department inspector general's office, told CBS that the February 2013 inspector general report had been heavily edited before its release.

Jen Psaki, then a spokeswoman for the State Department, said in response to the CBS report that "the notion that we would not vigorously pursue criminal misconduct...in any case is preposterous."

Fedenisn hired a Dallas-area law firm to represent her against the State Department after she was reportedly subjected to intimidation due to her whistleblower status.

That law firm was the victim of a break-in just weeks after the CBS report was published. The pair of thieves took only computers and files that contained information about Fedenisn, leaving untouched valuable items that included silver bars, the local Fox affiliate in Dallas reported.

Higbie said many whistleblowers like himself fear nothing will change if they take the risk to report wrongdoing.

"If a whistleblower reports a significant amount of criminal conduct that includes viable supporting evidence, some kind of action must be taken that is public," he said. "Otherwise, as is the case with the State Department, current and former employees do not believe coming forward with information that is vital to Congress in its oversight of the Department will materialize into any form of accountability."