The 34-year-old Wallabies winger was taken into custody by police on Friday over an alleged incident in Sydney's east on December 17 last year.
Police received a report that a 28-year-old woman was sexually assaulted at a licensed premises on Beach Road, Bondi Beach.
"Detectives from Eastern Suburbs Police Area Command took carriage of the matter and commenced an investigation under Strike Force Titheradge," police said in a statement.
Beale was arrested in a vehicle stop in Kingsford just before 2.30pm on Friday.
He was taken to Waverley Police Station for questioning and was later charged with two counts of sexually touching another person without consent, inciting another to sexually touch them without consent and sexual intercourse without consent.
He was refused bail to appear in Parramatta Bail Court on Saturday.
Beale took part in a 44-man Wallabies training camp on the Gold Coast last week and has appeared in close to 100 international test matches for the side.
He recently returned to Australia after several years spent playing in France ahead of the Super Rugby season for the NSW Waratahs.
Beale, from NSW, has spent most of his more than decade-long career with the Waratahs, aside from a brief spell with the Melbourne Rebels.
Rugby Australia, the NSW Waratahs and Rugby Union Players Association said in a joint statement they were aware of the situation regarding Beale.
"As this is a police matter, and we understand there has been no charge made, we will be making no further comment at this time," the statement said.
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