Mr Beale, 34, has played more than 90 games for Australia's national team, the Wallabies, over 10 years.
He was recently named in the Wallabies training squad for the World Cup.
In a statement, New South Wales Police said they arrested a man on Friday afternoon over the allegation and have charged him 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 and is due to appear in court on Saturday.
Local media have named the man as Mr Beale.
Rugby Australia said in a statement that it had suspended him from all forms of rugby "with immediate effect" in line with its code of conduct and would be carrying out its own investigations.
However, it will not be making any further comment as it is a police matter.
Mr Beale has played most of his career in Australia, but joined French team Racing 92 on a two-year deal in 2020.
At the end of his contract, he returned home to local team New South Wales Waratahs, with the hope of competing for Australia in a fourth World Cup in September.