The 55-test veteran hurt his ankle playing for the Queensland Reds in round 11 of the Super Rugby tournament and had carried the injury into training for the Wallabies' three-test series against France, the Australian Rugby Union said in a media release on Sunday.
"Scans late last week confirmed a pre-existing injury to the upper part of his ankle had not healed sufficiently and as a result medical staff from both the ... Wallabies and Queensland Reds agreed that surgery would be the best course of action," the ARU said.
Genia may be sidelined for up to eight weeks, which would leave him well short of match fitness for the Wallabies' Rugby Championship opener against New Zealand on Aug. 16.
Though rarely firing for the Reds this season, the 26-year-old's omission from the first two tests raised eyebrows, with his injury kept under wraps.
"Will has demonstrated enormous mental fortitude to play through the injury although it has reached a point where it's important he gets it surgically repaired so that he can get back to 100 percent fitness," Australia coach Ewen McKenzie said in the ARU statement.
"We've seen before how committed Will is when undergoing rehab and I would expect him to work hard to be available for selection when we begin our ... Rugby Championship campaign."
McKenzie has picked ACT Brumbies' Nic White as his starting scrumhalf against Les Bleus, with New South Wales Waratahs' Nick Phipps on the bench.
Australia edged France 6-0 in a dour contest in Melbourne on Saturday to seal the series 2-0 ahead of the final match in Sydney this week, but White had a poor game at Docklands stadium, missing three out of four penalty kicks and struggling to spark a haphazard Wallabies' attack.
Genia's withdrawal has opened the door for former Wallabies scrumhalf Luke Burgess to join the squad and add to his 37 caps.
The 30-year-old Burgess played his last test at the 2011 World Cup, but was in solid form for the Melbourne Rebels coming in to the June internationals.
(Reporting by Ian Ransom in Melbourne; Editing by Greg Stutchbury)
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