The State Department’s inspector general rebuked a senior adviser to Secretary of State Mike Pompeo on Thursday, saying the aide had played a role in reassigning a staffer suspected of being disloyal to the Trump administration.

The inspector general’s report recommended that Pompeo consider disciplining anyone who violates rules for assigning staffers based only on their merit.

The report cited a chain of emails among senior officials, including Brian Hook, the point man for Iran policy, and prominent conservatives following an article in the Conservative Review that characterized a staffer in the office as a “trusted Obama aide” who had “burrowed” into the State Department during the Trump administration. She was dismissed from Hook’s staff three months early, a decision the inspector general concluded was based not on merit but on improper, inappropriate and false perceptions of her political opinions, association with the previous administration and her national origin.

The State Department and Hook both condemned the conclusions as unfair.

The long-awaited report on political machinations in the Office of the Secretary took more than a year to complete and covers a period at the beginning of the Trump administration, when Rex Tillerson was secretary of state.

But it crystallizes the ongoing tensions that have bedeviled the State Department throughout the Trump administration, as political appointees have disparaged career professionals as “deep state” bureaucrats trying to undermine President Trump’s agenda. From the beginning of the administration, Democrats have complained that some officials, feeding off conspiracy theories promulgated by conservative activists, have spread false accusations in an attempt to purge the State Department and White House of apolitical diplomats and civil servants.

It comes on the heels of another inspector general report in August that reprimanded the leaders of the bureau overseeing international organization affairs for mistreating and harassing staffers. It said leaders had accused them of political disloyalty and retaliated against them.

The new report is imbued with a theme that has emerged in the House impeachment inquiry, in which veteran diplomats have spoken of political considerations infecting foreign policy decisions, particularly in the case of Ukraine.

The one complaint that permeates both inspector general reports and the unfolding impeachment inquiry is the mistreatment of professional staffers by political appointees.

Transitions between administrations — particularly those from opposing parties — are often filled with rough patches that eventually smooth over. But State Department veterans, who pride themselves on working through multiple administrations, say they have never experienced so much politicization as that imposed on Foggy Bottom in the Trump administration.

The latest report from the inspector general said the office had looked at five cases. But it said it found no evidence of inappropriate factors in two cases. It was unable to make any conclusion in two other cases, in part because of the “inability to gain essential information from key decision-makers” on the motives for personnel decisions. It found convincing evidence in only one case.

Although the report did not name her, the facts match the description of the treatment of Sahar Nowrouzzadeh, a State Department Iran expert who is of Iranian descent. Not long after Trump took office, she emailed Hook, asking for his help in countering and possibly correcting news reports that were wrong.

According to the report, her problems began after the Conservative Review published an article in March 2017, titled “Iran Deal Architect Is Now Running Tehran Policy at the State Department.” It stated, “Why Secretary Tillerson has decided to keep on a chief Obama policy official remains unclear.” The email was forwarded to State Department political appointees by at least four people, including Newt Gingrich, who had been emailed a copy by an adviser to former vice president Richard B. Cheney.

Nowrouzzadeh, who was born in the United States and joined the federal government in 2005 when George W. Bush was president, said the article misrepresented her background and made her fear for her job, as well as her safety. She asked Hook to help correct the article, but he did not reply to her.

In an eight-page response included in the report, Hook disputed many details of the inspector's report and denied that political factors played any role in his decision to replace Nowrouzzadeh with another Iran expert he had been recruiting already. He said the report was written in a "highly politically motivated and biased manner." The inspector general acknowledged that it had no emails from him stating any political motivations but said that did not fully explain why he agreed to remove her .

Hook said he had decided to make a personnel change before any internal discussion among other officials about the allegations. He said he neither knew nor cared about her political opinions, ethnic origin or previous work in the Obama administration.

“It would be wrong to graft the motives of anyone in the Department to my motives or to assume the motives of others were my motives,” he wrote.

The State Department also disagreed with the report, saying Hook made the decision purely for professional reasons. But it nevertheless agreed to establish a training course to address standards of conduct and discuss prohibited personnel practices.

“The Secretary and the entire leadership team of the Department are committed to ensuring the highest levels of professional behavior on behalf of all the staff here at the State Department,” said the response written by T. Ulrich Brechbuhl, a senior adviser to Pompeo.

In a statement released by her lawyer, Nowrouzzadeh said she was hopeful her case would help deter misconduct in this or future administrations.

“For nearly 15 years, I’ve been proud to serve our country, across Republican and Democratic administrations,” she said. “I continue to strongly encourage Americans of all backgrounds, including those of Iranian heritage, to consider public service to our nation and to not be discouraged by these findings.

“I also think I speak for many within what President Harry S. Truman during a critical time in U.S. history called ‘the most loyal body of civil servants in the whole world’ in saying that we should not fear, but rather value rigorous debate among colleagues with deep experience when formulating U.S. policy on matters critical to our national security. It is one of the ways we faithfully discharge our duties, as per our oaths and loyalty to the U.S. Constitution, above all else.”