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Amid reports of alcohol-related issues, the ARU said Beale, 24, would enter a private health facility to undertake counselling for his problems.
Beale has been in continual off-field strife this season and was suspended by the Rebels for striking team-mates Cooper Vuna and Gareth Delve during the club's tour in South Africa on March 23.
The latest development comes just weeks before the British and Irish Lions arrive in Australia for their three-Test tour.
The ARU issued a statement after meeting with Beale's Super Rugby club Melbourne Rebels and the Rugby Union Players' Association (RUPA) on Monday.
"Kurtley has done this with the backing of ARU, RUPA and the Melbourne Rebels, who congratulate him on this decision to seek assistance," the statement said.
"Any future selection will be dependent upon successful completion of his treatment programme."
Beale was stood down from last weekend's 36-32 loss to the Blues in Auckland for breaking the terms of his rehab agreement by drinking the night after his return to action against the Chiefs in Melbourne, reports said.
As a condition of his return Beale had agreed to an off-field programme to deal with alcohol-related problems after discussions between the ARU, the Rebels and RUPA.
The ARU said any future selection of Beale at a club or national level would be dependent on successful completion of his treatment programme.
The latest setback appears to have ended the talented playmaker's chances of taking part in the British and Irish Lions series starting in Brisbane on June 22.
Beale was omitted from last month's preliminary Australian squad and he is unlikely to be named when coach Robbie Deans announces his final Wallabies squad on Sunday.
The Wallabies play three Tests against the Lions from June 22 to July 6.
