Perth Bears general manager of football Gareth Holmes will serve as interim chief executive after Anthony De Ceglie resigned Friday evening, weeks before preseason training.
The departure followed a breakdown in relations with the board, which reportedly no longer supported De Ceglie.
ARLC executive chairman Peter V'landys had selected the former Seven West Media director before the board was established and lobbied for a three-month reprieve.
His intervention last week bought time, but the sides could not resolve their differences.
V'landys told News Corp: "He has set up the club perfectly so I have no concerns because the foundations are all there."
The Bears are scheduled to enter the NRL in 2027.
Coach Mal Meninga had dismissed speculation about De Ceglie's future before the resignation, saying: "We don't want to fight any external battles."
In a club statement, De Ceglie praised Meninga and assistant Ben Gardiner: "The club is in exceptional hands under the leadership of head coach Mal Meninga and assistant coach Ben Gardiner."
The exit adds to upheaval following inaugural head of football David Sharpe's departure and criticism over the club's failure to secure a marquee signing.
De Ceglie's appointment was viewed as important for building media attention in AFL-focused Perth.