The veteran fullback, who returned to Australia last year after a stint with French Top 14 side Racing 92, was arrested and taken to a Sydney police station on Friday afternoon.
New South Wales Police said a man had been charged with "two counts of sexually touch another person without consent, incite another to sexually touch them without consent and sexual intercourse without consent".
He was widely reported to be Beale, who recently became a father. The alleged assault occurred in December.
"The man was refused bail to appear before Parramatta Bail Court tomorrow," police said.
Beale, 34, returned to Sydney and the NSW Waratahs to keep himself in the frame to play for Australia at a fourth World Cup this year.
Should he do so, he will join George Gregan and Adam Ashley-Cooper as only the third Australian to feature at four tournaments.
"Rugby Australia, the NSW Waratahs and Rugby Union Players Association (RUPA) are aware of the situation involving Kurtley Beale," Rugby Australia said in a brief statement after the arrest.
It said the three bodies would not make any further comment while the matter was being handled by police.
Beale has played 95 Tests and took part in a Wallabies training camp on the Gold Coast this month. Coach Dave Rennie has since been fired and replaced by former England boss Eddie Jones.
