The 36-times capped Beale hit the headlines for all the wrong reasons earlier in the season when he stuck teammates Cooper Vuna and Gareth Delve in South Africa on 23 March. That led to an indefinite suspension and a series of counselling sessions.
He returned to action against the Chiefs on 3 May, scoring a try after coming off the bench in a 39-33 home defeat, but then fell foul of the terms of his rehab.
"Qantas Wallabies playmaker, Kurtley Beale, will take an indefinite leave of absence from playing to seek assistance in resolving personal issues. Kurtley has voluntarily entered a private health facility in order to undertake counselling," read the ARU statement.
"He has done this with the backing of ARU, RUPA and the Melbourne Rebels who support him on this decision to seek assistance.
"Any future selection will be dependent upon successful completion of his treatment program. Kurtley has requested that his privacy be respected at this time."
Qantas Wallabies coach Robbie Deans is due to name the first 24 players in his squad to take on the Lions this weekend and then now seems no chance of Beale being included. The Rebels are due to face the tourists in Melbourne on 25 June - three days after the 1st Test in Brisbane.
The Rebels have won only two of their 11 games to date and lost another of their star back line players, James O'Connor, last weekend with a chest injury. The 22-year-old is likely to miss the next two weeks of Super Rugby action after damaging his left sternoclavicular joint, but should be fit to face the Lions.