The Melbourne Rebels playmaker was the front-runner to wear the number 10 jersey for the June series before suffering the injury in Friday's Super Rugby loss to the Hurricanes.
Wallabies coach Robbie Deans broke the bad news on Monday but said it was too early to tell how long the 23-year-old will spend on the sidelines.
"Kurtley had an appointment this morning with a specialist and he's going to require an operation," Deans said.
"The full extent of the damage won't be known until the surgeon gets in.
"But the fact that he needs an operation is indicative of the fact that it is serious and it will rule him out of the June (Test) window."
Beale's absence will see Reds star Quade Cooper get first crack at the fly-half position, despite having played just one-and-a-half games since knee surgery last November.
The enigmatic fly-half was initially going to be rested from the Tests but injuries to Beale and James O'Connor (lacerated liver) have opened the door for a sooner-than-expected return.
And the 24-year-old is ready to go if selected to face Scotland in Newcastle next Tuesday.
"I'm very confident, I've only played one game and a half and I felt good while I was out there, so it's a matter of just keep ticking the boxes and keep moving along," Cooper said at the team hotel in Sydney.
"If I get the opportunity I'll put my hand up and give it everything I've got.
"I've done a lot of hard work over these seven months that I've been out and the reason you do all that is for opportunities like this.
"I'm just happy to be part of the Wallabies squad moving forward and hopefully I just keep improving as I go along."
Utility man O'Connor will train with the Wallabies in Sydney this week but will also miss the one-off Test against Scotland on June 5 and the three-Test series against Wales.
Skipper James Horwill is also expected to miss the June fixtures with a hamstring injury suffered in the Reds' victory over the Brumbies.
However, Deans revealed the injury may not be as serious as first feared.
"James, we are presuming, is out as well for the whole of June but it's not as bad as it first looked - it looked pretty sinister," Deans said.
"I understand it's a middle-belly hamstring tear. It's also the same leg he had the graft for his knee operation so it could simply be scar tissue being removed.
"He's certainly hopeful that's it's not too bad, he feels a lot better than he did in the first instance because the sensation at the time wasn't that good, from all accounts."
Deans will name his stand-in captain on Sunday, with David Pocock expected to pip Will Genia for the job.
The 22-man squad to face Scotland will also be confirmed on Sunday.
Meanwhile, Deans insists former skipper Rocky Elsom's Test career is not over after the 29-year-old was left out of the initial 39-man training squad.
"There's clearly a fitness component (to his non-selection), I mean Rocky hasn't played much rugby and he didn't play this recent weekend so that's a big part of it," Deans said.
Asked if he still sees Elsom as a Test player, Deans added: "More importantly I hope Rocky sees himself as part of it (the Wallabies' future) because he's perfectly capable of it.
"And if that's something he's still passionate about that's something he can get done."
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