The Wallabies are in Argentina preparing to play the Pumas in Mendoza on Saturday and Beale was left out of the match-day squad after coming off the bench against South Africa last week.

"We're aware of an alleged incident involving Wallabies player Kurtley Beale on a flight from South Africa to Brazil on Sunday," an ARU spokesperson told the Daily Telegraph.

"The matter has been referred by team management to the Australian Rugby Union's Integrity team to be investigated according to our usual processes.

"This investigation will ensure all parties have an opportunity to present all relevant facts, before any assessment of the alleged incident can be reached. We expect the investigation will be completed by the end of next week.

"We can confirm that a Wallabies staff member has left the team to return to Australia."

Coach Ewen McKenzie spoke to journalists with the Wallabies team in Mendoza and said the situation was "complicated".

"A staff member's flown home but I'm not going to comment on the detail of that," McKenzie said.

"Matters of integrity, you've actually got to protect the people involved until there is some sort of decision. So there's processes going on and, as I say, it's awkward when you're [on the other side of the world].

"But welfare and these matters are paramount from my perspective, and behaviour, you already know how I've done these things in the past. I don't leave these things unattended to," McKenzie said.

Beale's 47-test career has been dogged by a succession of off-field problems and last year the 25-year-old was forced to undergo counselling and rehabilitation for his struggles with alcohol.

The NSW Waratahs playmaker is off contract for next season and has yet to agree on a new deal with the ARU.