Over all, Yale University has made progress in its treatment of women, especially undergraduates, since 2010, when fraternity members on the quad chanted, “No means yes, yes means anal” — leading to an investigation by the federal Department of Education’s Office for Civil Rights. That investigation is over, and the university has a Title IX coordinator responsible for ensuring gender equity and a sexual misconduct committee, which heard the complaints against Dr. Simons. Yet at the medical school, many faculty members say little has changed.

A dozen faculty members — male, female, senior and junior — talked with a Times reporter last week about their distress over the school’s handling of the Simons case on the condition that the conversation be in a group and that most participants not be quoted directly.

One participant, Joan Steitz, a prominent molecular biologist, was an exception, saying that in recent years, she had been “very disappointed” by what she sees as the medical school’s lack of progress in ensuring equality for women on the faculty and its lack of openness on decision-making.

Some medical school professors question the value of the universitywide committee, even with its outside fact-finders and trained members from across the university’s different schools, given that the provost can overturn its recommendations, without disclosing them or saying why he rejected them.

Dr. Simons and the school have their defenders: As word spread last week about The Times’s queries, two women on the faculty at the research center contacted The Times to say that he had been an outstanding leader who had promoted women, and that the accusations had been blown out of proportion.

Since the reduced suspension of Dr. Simons was announced last November, senior women on the faculty and, separately, junior women in the cardiology department had taken their concerns about his expected return in June 2015 to Dr. Salovey, the university president.

In a follow-up letter to the president, the senior women said the climate for women at the medical school had “substantially deteriorated under the current leadership.”