Rugby Australia chief executive Raelene Castle resigned on Thursday after she said the board of directors made it clear that it would not allow her to continue in her role.
Rugby Australia said Castle informed chairman Paul McLean of her decision.
"I love rugby on every level and I will always love the code and the people I have had the honor of working with since I took this role," Castle said in a Rugby Australia statement.
"I made it clear to the board that I would stand up and take the flak and do everything possible to serve everyone's best interests.
"In the last couple of hours it has been made clear to me that the board believes my no longer being the CEO would help give them the clear air they believe they need. The game is bigger than any one individual." Castle was under pressure to retain her position as Australian rugby faced multiple challenges, including a damaged relationship with top players.
Professional rugby players around the world have been forced to accept substantial pay cuts to help the sport survive the massive blow delivered by the coronavirus outbreak. Super Rugby is suspended and the Rugby Championship involving Australia, New Zealand, South Africa and Argentina is unlikely to go ahead.
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World Rugby chairman Bill Beaumont last week expressed doubt that any professional rugby competitions will be able to resume in 2020.
Rugby Australia also became embroiled in a protracted public and legal row with its star player, Israel Folau, after he posted religious commentary on his social media account at odds with the sport's values.
This week, a number of former Wallabies captains sent a letter to the board demanding a change of administration, saying the sport had lost its way.