ARU chief operating officer Rob Clarke has resigned.
Clarke was believed to be earmarked as a potential successor to CEO Bill Pulver, after stints with the Brumbies and Rebels as well as the national body spanning more than a decade.
A former advertising CEO, Clarke returned to the ARU in 2014 as general manager of professional rugby, operations and marketing.
His elevation to chief operating officer in 2016 was his second stint in the role.
A widely respected figure among the rugby community, as second-in-charge at a national level, Clarke had been at the forefront of a turbulent time in Australian rugby.
Clarke was forced to respond to criticism from Western Australia in recent weeks over his links to the Rebels and Brumbies, as the ARU comes to a final decision about its Super Rugby composition in 2018.
The ARU released a statement on Thursday afternoon, with ARU Bill Pulver paying tribute to Clarke.
"His resignation was difficult to accept but Rob has decided the time is right to pursue a different course along with his family and he deserves to be incredibly proud of his career in the game," the statement read.
"When I look at the values of our game it is hard to imagine someone who embodies those values both in a professional and personal sense more than what Rob does. He is a tremendous loss for the organisation.
"I am ever-grateful to Rob for his contribution to the ARU and I wish him the very best for his future."
Clarke will finish his role in June, and the statement said he would not be making any comment until after a final decision was made on the future of Australia's Super Rugby teams.