Wallabies skipper Stephen Moore has been ruled out for the rest of the year after being told he needs a knee reconstruction.

In a massive blow for Australia, scans have shown that Moore ruptured his anterior cruciate ligament and medial ligament in the opening minute of Saturday night's 50-23 win over France.

The 92-Test hooker injured his left knee after falling awkwardly in making a tackle from the side on French flanker Bernard Le Roux.

Moore bravely attempted to play on but was a mere passenger as France pressured inside Australia's half before Frederic Michalak slotted a drop goal.

The new skipper featured in all 15 Tests last year but had to be replaced by Tatafu Polota-Nau and finished the night in hospital having scans.

It is also a major disappointment for the Brumbies who are sitting in the top six in Super Rugby and now have to do without their hard-nosed rake for the remaining three rounds heading into the finals.

"The whole year is gone ... he's obviously shattered," coach Ewen McKenzie said on Sunday.

"It leaves a bit of a void because we had put a lot of things in the pipeline."

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The Wallabies captaincy is fast becoming the most unwanted job in world rugby.

Moore's injury follows the season-ending injuries in 2012 that afflicted James Horwill (hamstring), David Pocock (knee) and Will Genia (knee), who were all appointed to the role by former coach Robbie Deans.

Moore was also McKenzie's third captain in quick succession after he dumped Horwill from the role on their season-ending tour of Europe last year and replaced him with loose forward Ben Mowen.

Mowen, however, was not considered for the squad this season given his impending departure from Australian rugby following the Super Rugby season.

McKenzie named backline stalwart Adam Ashley-Cooper and openside flanker Michael Hooper as vice-captains before the series.

Hooper is likely to take the reins going forward after he took over the captaincy when Moore left the field on Saturday.

In a double-blow for the Wallabies, lock Sam Carter, who made his Test debut against France, will also miss the rest of the series with a high ankle strain, McKenzie confirmed.

AAP/Reuters