Berrick Barnes is unlikely to know before the weekend whether he will miss the Wallabies' grand slam tour of the UK and Ireland after being ruled out of Saturday's Bledisloe Cup Test against the All Blacks with an ankle injury.

In a massive blow to Australia's chances of avoiding their first 4-0 series whitewash against New Zealand since 1962, Barnes was rushed to hospital in Tokyo on Thursday for emergency scans after hearing a crack when he rolled his left ankle at training.

Initial fears were allayed when x-rays later cleared the newly-appointed Wallabies vice-captain of a fracture.

But the Australian team's medical staff say Barnes probably won't know the full extent of his injury until the swelling subsides in the next 24-48 hours.

It was hoped he had not suffered major ligament damage, which would almost certainly rule Barnes out of the Wallabies' first grand slam tour in a quarter of a century.

"If it's just a ligament injury in isolation, it might be just a couple of weeks. He will stay with us if it's a two or three-week injury," Wallabies coach Robbie Deans said.

"If it's syndesmosis, that's more sinister." Should he be sent back to Australia, it would be a devastating personal blow to the 23-year-old midfield general, as well as a huge setback to the Wallabies' prospects of completing a grand slam sweep of England, Ireland, Scotland and Wales.

Barnes lasted less than 20 minutes of last year's spring tour of Europe before breaking down against Italy in Padova with a knee injury that required an early flight home.

The Wallabies have already sent young outside back Rob Horne home this week after he suffered a recurrence of his chronic hamstring injury, with Brumbies centre Tyrone Smith joining the squad on Thursday.

More immediately, Barnes' scratching from Saturday's Test prompted Deans to reshuffle his backline, promoting teenager James O'Connor to start at fullback and moving Adam Ashley-Cooper to inside centre.

Quade Cooper has replaced O'Connor on the bench, while star five-eighth Matt Giteau will assume the vice-captaincy.

The Wallabies were confident they could overcome the disruption, but also naturally disappointed for the luckless Barnes.

"I hope he's alright," winger Digby Ioane said.

"I heard he's going to be alright in two weeks, but I'm not sure. I hope he comes back as soon as possible.

"It is a big loss because he is the go-to man, along with Matt Giteau. They can mix it up and change between five-eighth and 12.

"But Coops is dangerous on the ball. He's more of a go-forward man; he can break the line and stuff, whereas Barnesy's more of a ball player, a smart player.

"The good thing about us is we've got some depth. We've got guys like Coops who can play anywhere and there's a lot of boys in that situation." Ryan Cross, who will now partner Ashley-Cooper in the centres, said while Barnes' withdrawal would change the dynamics of the Australian backline, and prompt some tactical changes, he was confident the Wallabies would recover.

"We've been training well and everyone's ready to go. Obviously you don't want this to happen but hopefully we can adapt," he said.

"Berrick and Gits share the load a bit so it's going to be up to the rest of the backline to take up what Berrick was doing.

"Adam's got a bit of a kicking game and James O'Connor's pretty good there, so we've still got options there.

"Hopefully it won't change things too much." Wallabies: James O'Connor, Peter Hynes, Ryan Cross, Adam Ashley-Cooper, Digby Ioane, Matt Giteau, Will Genia, Wycliff Palu, David Pocock, Rocky Elsom (capt), Mark Chisholm, James Horwill, Ben Alexander, Tatafu Polota-Nau, Benn Robinson. Replacements: Stephen Moore, Matt Dunning, Dean Mumm, George Smith, Luke Burgess, Drew Mitchell, Quade Cooper.