Beale was already facing disciplinary charges over a bust-up with a team official on a flight from South Africa to Argentina for a Rugby Championship test last week but that issue was now "a secondary matter", ARU chief Bill Pulver said.
"This matter relates to Kurtley Beale allegedly distributing what we consider highly inappropriate and deeply offensive text messages and images to a number of people in June, referencing an ARU staff member," Pulver told a news conference.
"We became aware of this incident this week and believe an independent tribunal is the appropriate forum for these allegations to be considered."
The 25-year-old, who has played 47 times for his country, would not be considered for selection for Australia until an impartial "Code of Conduct Tribunal" reached a conclusion, Pulver said.
That means he will definitely miss the test against New Zealand in Brisbane on Oct. 18, for which coach Ewen McKenzie will name his squad on Friday.
Beale, who started the Rugby Championship as first choice flyhalf, had in any case been dropped for the final match of the competition against Argentina in Mendoza, which resulted in a 21-17 victory for the Pumas.
That match had been overshadowed by the mid-air row between Beale and team business manager Di Patston, which was reportedly triggered when the player was asked to change his shirt.
Patston returned home early from the tour and is now on indefinite sick leave.
CULTURE AND DISCIPLINE
Pulver would not disclose whether Patston was also the victim of the offensive text messages and said they had come to the ARU's attention "concurrent with" and not "as a result of" the investigation into the airplane spat.
"My understanding is they were shared with members of the team environment, not sure who," Pulver said. "However, it was inadvertently sent to the employee concerned."
Beale has rejuvenated his career this season with the Super Rugby champion New South Wales Waratahs after a troubled 2013.
He was stood down by Melbourne Rebels last year for punching two team mates in the wake of a defeat in South Africa and then suspended indefinitely after breaching team alcohol protocols.
He also spent time in rehab for "alcohol issues" in his home city of Sydney.
If Beale is found guilty of sending the offending messages he could face having the remainder of his ARU contract torn up, as happened to his friend and fellow back James O'Connor last year when he was involved in a drunken row at Perth airport.
That would only the increase the likelihood of Beale, who has yet to renew his ARU contract for next year, moving to rugby league or to play union in the lucrative French league - either way ruling him out of the 2015 World Cup.
Pulver said overall he was happy with the discipline in the Wallabies squad under McKenzie, who he described as a "great coach".
"Clearly culture and discipline are very successful components of a successful team environment and by and large I believe we've got that," he said.
