Beale, who has had a torrid year with several off-field problems, played in all three tests in the British and Irish Lions series but has been carrying the injury since last year.
"It's pretty simple, Kurtley's had a shoulder injury for more than a year now," McKenzie, who took over from Robbie Deans after the Lions series defeat, said on Friday.
"As a result, he's missed some football. I've been talking to the medical side of the business and there's a lot of guys carrying damage.
"When you're carrying a shoulder injury for a long period of time it has an impact on your game. We felt the best thing for him was to get it fixed.
"By doing it now it allows him the opportunity of a pre-season and then he can play a lot of Super Rugby and be 100 percent to play test football next year," added McKenzie, who gave Beale his Super Rugby debut when he was still a teenager.
Beale, capped 39 times for the Wallabies, is almost certain to re-sign with the New South Wales Waratahs over the next month and draw a line under his troubled two years with the Melbourne Rebels.
The richly-talented 24-year-old's unhappy time in Melbourne culminated in a drunken assault on captain Gareth Delve and team mate Cooper Vuna in South Africa in March.
Another infraction of the team's disciplinary code saw Beale stood down indefinitely by the Rebels and return to his home city of Sydney to undergo counselling for issues relating to alcohol abuse.
Even the Lions series was not without off-field incident for Beale, who was photographed with team mate James O'Connor at a fast food restaurant during the week of the second test.
The failure to control the antics of the pair was behind some of the criticism of Deans, who departed in the wake of the 41-16 hammering in the third Lions test.
(Editing by Amlan Chakraborty)
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