In May 2020, Rathjen commenced an indefinite leave of absence after University of Adelaide Chancellor Kevin Scarce resigned without public explanation the previous day. Later in the week, the Independent Commissioner Against Corruption (ICAC) confirmed he was investigating allegations of improper conduct by the Vice-Chancellor of the University of Adelaide. Rathjen, accused of engaging in "a personal relationship with a staff member", was succeeded by Acting Vice-Chancellor Mike Brooks. Rathjen formally resigned in July 2020, "due to ill health". In August 2020, the ICAC found that Rathjen had committed "serious misconduct" by sexually harassing two University of Adelaide colleagues, had lied to the then Chancellor Kevin Scarce, and also lied to the Commissioner in his evidence with respect to an investigation of sexual misconduct with a postgraduate student when he was employed at the University of Melbourne. The ICAC Commissioner Bruce Lander acknowledged there were "further issues" in the full 170-page report on the investigation which he chose not to release due to privacy concerns surrounding the victims, instead releasing an abridged 12-page version 'Statement about an Investigation: Misconduct by the Vice-Chancellor of the University of Adelaide'. In determining his findings, the Commissioner relied in part on the personal blog of US journalist Michael Balter who documented Rathjens prior history of sexual harassment, and was largely responsible for bringing the matter to the public's attention, and ultimately ICAC's. The ICAC Commissioner's damning findings against Rathjen have put the University of Adelaide's culture under intense scrutiny in both the local and international media.