He served as the head of the university's Harry S. Truman Research Institute for the Advancement of Peace until January 2007, and also taught the Introduction to Anthropology course, making him well known to students.
[5] Ben-Ari's troubles with the law began when a number of students sent an anonymous e-mail to university authorities, accusing him of rape and of threatening to withhold their research funding if they refused to have sex with him.
An editorial in Haaretz criticised the media for their sensationalistic reporting of the prurient details of the incident, as compared to the lack of fanfare with which they announced that no charges would be filed.
[12] He had been scheduled to take up lecturing duties again at HUJI in early 2009, teaching one undergraduate course about family and education in Japan, and one graduate course about anthropology in Israel; however, he volunteered to delay his return while the case against him was still open.
[15] In late February 2011, the university formally announced that Ben-Ari would be suspended for two years without salary or right to use research funding, and requested the Jerusalem District Prosecutor's Office look into the possibility of reopening the criminal case against him.