She said her office would spend the next few months to a year interviewing students, faculty and others to assess whether the campus was a hostile environment.
"We will use all of the tools at our disposal," she said.
Title IX ensures equal rights at educational institutions that receive federal funding. If the prestigious university is found to be non-compliant and doesn't fix the problem, it could lose more than $500 million in federal funding. Ali said a school rarely had its federal funds pulled.
In a paper statement, the university said, "Yale does not and will not tolerate sexual harassment and seeks to build an environment that is supportive of women and men."
Hannah Zeavin, a Yale junior and a complainant, said the group of 16 felt it should change the current Yale environment to one that's less hostile to women.
"If everywhere you turn, there's someone who has violated another person's bodily agency and they're near you, how are you supposed to go about having those bright college years?" she said.
"We love our university," Zeavin said. "We want to see that change happen."
The Associated Press contributed to this article.