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 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. The full extent of the damage won't be known until the surgeon gets in," Deans said.
"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," he added.
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."
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."