A scientist who is a leading expert on leeches was fired this month from his curator’s post at the American Museum of Natural History after the museum found that he had sexually harassed and bullied a graduate student who was doing research under his supervision.

The museum cited the research adviser, Mark E. Siddall, for having violated a museum policy that prohibits sexual relationships between museum staff and mentees who are under their academic supervision.

The student had told external investigators hired by the museum that Dr. Siddall had sexually assaulted her at the museum in April 2019, made sexual comments to her and sent “inappropriate” text messages, museum officials said in a document that outlined their findings in the case. Museum officials told the student in a letter that they had found that the scientist “engaged in verbal, written, and physical conduct of a sexual nature that had the effect of unreasonably interfering with your academic performance.” But they did not find Dr. Siddall responsible for sexual assault.

The museum also found that, after a breach in the scientist’s working relationship with the graduate student, he “compromised an academic publication,” on which she had worked, according to the document on their findings.

Dr. Siddall has denied the accusations and defended himself in an email as a “lifelong champion of women in science,” citing the fact that over a period of years, 17 out of his 21 undergraduate mentees had been women.

He said that he disagreed with the findings that led to his dismissal, but he had not appealed “for personal and family reasons and because of mounting legal costs.”

Twice in recent years, other officials affiliated with museum have been publicly accused of sexual misconduct, most recently last year when astrophysicist Neil deGrasse Tyson became the subject of an investigation by a company hired by the museum. Dr. Tyson, who leads the museum’s Hayden Planetarium, denied the accusations and the museum ultimately determined that he could keep his job.

The museum has said it recently bolstered its process for reporting harassment and discrimination by updating policies and training programs. Still, several current and former employees said in interviews that they did not think the institution was as aggressive or transparent as it should be in these matters, a position that the museum denied.

“In this case, the Museum investigated and resolved the complaint swiftly, and the sanction was immediate termination,” said a museum spokeswoman, Anne Canty, referring to the graduate student’s complaint. “The process worked as it was designed to.”

Dr. Siddall, 53, an invertebrate zoologist, worked at the museum for 21 years. He is a former president of the American Society of Parasitologists and was director for one of the museum’s undergraduate research programs. Online, he calls himself the “leech guy” because of his research focus on the bloodsucking parasites.

The student, who is in her 20s and did not wish to be named out of fear of professional retaliation, said in an interview that she filed an official complaint against Dr. Siddall in May. That prompted the museum to retain the law firm of Kaplan Hecker and Fink to look into the student’s account that she was assaulted in a nonpublic area of the museum, according to the letter from museum officials to the student explaining their determination in the case.

She said in her own letter to museum officials that the scientist had made advances on her during an encounter at the museum and pressured her into giving verbal consent and drinking alcohol. She described the encounter as an assault to investigators, according to the letter from museum officials.

In an emailed statement in response to questions on Tuesday, Dr. Siddall said that the student had initiated a physical encounter, which he said he had rebuffed, and he denied there was any assault. He said he had subsequent emails and text messages from the graduate student that indicated that she never “felt anything was inappropriate or coercive.”

The student said she kept a cordial, sociable demeanor with Dr. Siddall to avoid starting a conflict and potentially putting her career in danger. In the statement she sent to museum officials, she wrote that Dr. Siddall “was in a position of power where he could take advantage of me by putting me in a situation where I had to either decline his sexual advances (risking making him angry and putting my Ph.D. project into jeopardy) or be forced to submit to unwanted sexual contact.”

The bullying finding revolved around the events from the spring of this year, shortly before the student filed the complaint. The student told investigators that after their professional relationship eroded, Dr. Siddall made “repeated efforts” to prevent her from publishing a paper that included research she had completed under his supervision at the museum, according to the museum’s summary letter.

Dr. Siddall said in his statement that part of the conflict involved the fact that he had found a serious error in the paper’s findings and suggested that his name could be removed if it was going to be published in its flawed form.

But the museum officials backed the student. In the letter to the student that explained their findings, dated Aug. 13, museum officials wrote that, “Although Dr. Siddall did find errors in the publication that needed correction, the museum has concluded that Dr. Siddall’s efforts were motivated at least in part by impermissible efforts to punish you for your refusal to continue to engage with him directly and in the inappropriate manner which he had engaged with you in the past.”

Susan Perkins, a former museum curator who is now the dean of science at the City College of New York, said in an interview that she had filed a complaint with the museum in 2017 saying that for over a decade, Dr. Siddall had frequently berated her over email in a way that she found to be unprofessional — first as her postdoctoral adviser and then as her colleague.

Dr. Perkins said that he often chastised her over email about work-related issues then acted as though nothing had happened, creating a cycle that she eventually recognized as “abusive” and a toxic workplace environment. In the end, Dr. Perkins said that the museum found that Dr. Siddall had not violated any of the institution’s policies.

Dr. Siddall said in his statement that he had several conflicts with Dr. Perkins and that he had filed a countercomplaint against her. He said the dispute was “thoroughly investigated by an outside firm, which exonerated me in full.”

“My feeling was, ‘how could they think nothing wrong had happened?” Dr. Perkins said. “I didn’t have expectations that Mark would be fired, but I was disappointed that the end result was that he had done nothing wrong.”

Susan Beachy contributed research.

10/2 — This article has been updated to reflect Dr. Siddall’s assertion that he rebuffed a physical encounter initiated by the student.