The report applauded Johnson's efforts to reach out to staff and found his leadership improved after the previous deputy chief of mission, an embassy's second-in-command, departed.
But amid media reports that Johnson made sexist and racist comments, the OIG said it "learned, through employee questionnaires and interviews, that the Ambassador sometimes made inappropriate or insensitive comments on topics generally considered Equal Employment Opportunity (EEO)-sensitive, such as religion, sex, or color."
The report did not offer specifics, but it recommended that the State Department's Office of Civil Rights investigate further.
More broadly, the OIG said Johnson "did not always model the Department's leadership and management principles... regarding communication and self-awareness." It faults him for casting any hesitation or push back from career diplomats as "resistance" and at times questioning embassy staff's motives or tacitly threatening to have them replaced.
"This caused staff to grow wary of providing him with their best judgment," the report found, adding his "demanding, hard driving work style... had a negative effect on morale."
But the report notes that improved when a new deputy chief of mission took over in January 2019, who worked better with Johnson than Lew Lukens, a senior Foreign Service officer who had previously served as U.S. ambassador to Senegal and to Guinea-Bissau.
The report also commends applauds Johnson's effort to reach out to staff and get "to know them better, to convey his appreciation for their work, and to continue to familiarize himself with the many aspects of the complex, multi-agency mission he was leading."
Johnson himself took issue with the report's finding about "insensitive" remarks, writing in a May 27 letter to the OIG, "If I have unintentionally offended anyone in the execution of my duties, I deeply regret that, but I do not accept that I have treated employees with disrespect or discriminated in any."
"I believe that team cohesion in our mission is better than ever," he added, noting the "absence of any official complaints against me" by staffers.
Both he and State Department leadership rejected the OIG's call for an Office of Civil Rights assessment. Acting Assistant Secretary of State for Europe Phil Reeker told the OIG in a July 1 memo that Johnson is "well aware of his responsibility to set the right tone for his mission and we believe his actions demonstrate that."
The department said that Johnson watched a video on workplace harassment, had senior embassy staff do the same, and encouraged personnel to take unconscious bias training.
But the OIG was not satisfied with that response -- leaving the issue "unresolved" in its final report and reiterating that Johnson's behavior should be independently assessed.
While the 43-page report focuses on several other issues, from locally employed staff's pension fund to consular office layout, it does not touch on Johnson's alleged outreach on behalf of President Trump to persuade the British government to hold the British Open at his golf course and resort in Scotland.
Johnson told colleagues that Trump personally asked him to do so, according to Lukens, who was in his role at the time but later pushed out. Lukens told ABC News that he counseled Johnson that it would be unethical, but that Johnson did it anyway and raised the issue with the U.K.'s secretary of state for Scotland, David Mundell.
Trump denied that was true, and the British Open has not been held at Trump Turnberry. A U.K. government spokesperson told ABC News, "Mr. Johnson made no request of Mr. Mundell regarding the British Open or any other sporting event."
The OIG report said Johnon's "in-country outreach activities" were deemed "consistent" with his "duties to develop local contacts and potential leaders," but it's unclear if that includes any alleged efforts related to Trump Turnberry or whether the OIG investigated the issue in this report.
ABC News's Katherine Faulders contributed to this report.