"I know that's your mentality to think everything is a cover-up, but it's not, I want to be really clear", Cheika told reporters.
Cannon, who has worked until recently as a rugby commentator, says Cheika's team selections have been "bewildering".
Rugby Australia has backed Cheika until his contract expires at the end of the 2019 World Cup in Japan.
But the Wallabies' team rules state guests are not allowed in players' rooms.
"So our leadership group came to me about it earlier in the week and asked me to deal with it in a way I thought appropriate".
Both Beale and teammate Adam Ashley-Cooper have been stood down for this weekend's Test at Twickenham after breaching team protocol.
Australian media reported that three women, one of them Ashley-Cooper's sister-in-law, joined the pair for drinks in the hotel bar and then went to their room to order some food.
After being thumped 37-18 by England on Saturday coach Michael Cheika has issued a defiant promise that Australia will be all the better for their bad 2018 and that he fully expects them to challenge for the World Cup in a year's time.
UAE signals jailed UK academic could be freed in 'amicable solution'
Another Conservative MP Johnny Mercer called on Britain to re-examine its military ties with the UAE following Hedges' sentencing. Mr Hedges, originally from Exeter, was arrested at Dubai Airport as he tried to leave the country on May 5.
Cheika said he believed such sanctions are more effective when kept private.
Cheika - who was world coach of the year in 2015 having pulled a demoralised squad up by its bootstraps in lss than a year and guided them to the World Cup final - said painful experiences in rugby is part and parcel of the sport just as it is in life. "I spoke to the boss about it and she understands that it's like punctuality, curfew or any of those things within a team".
"If the skipper says that's not happening or that's the team rule no matter what it is, you go against it no matter what it is, whether in this instance it was a family member or whatever it is, doesn't matter, that's the rule". You've got rules in place, you've got a line in the sand, and that's the line in the sand that Michael has used and you've got to live by it.
He has been playing in the number eight position to accommodate Hooper on the flank, but has won the majority of his 77 caps on the side of the scrum.
"I didn't hear that", Hooper said.
Having been impressed by the likes of Will Skelton, who has been transformed since joining Saracens from the Waratahs previous year, Dwyer also believes the improved condition and form of some players overseas is an "indictment" on the Australian Super Rugby scene.
"We've got one of the best doctors in world sport in Nathan Gibbs".