Clarke is still in London receiving intensive treatment on his troublesome back injury, meaning Bailey will again lead the side in Wednesday's must-win Champions Trophy clash against New Zealand at Edgbaston.
"It's something we've been preparing for," he said after Clarke was formally ruled out. "I don't think 'Pup' was ever going to come in and play a game without having trained, so I think everyone assumed what was going on."
Bailey added: "He's our captain and our best batsman. We miss him every time he's not with us.
"But as any team does when your best players are out, the challenge is for someone to step up and fill the hole, or numerous people to fill the hole."
Australia's main problem appears to be a misfiring top order. They were dismissed for 65 by India in a pre-tournament warm-up and fell well short of chasing a winning mark of 270 against England in their opening fixture.
But Bailey is adamant he expects them to face New Zealand in a confident frame of mind.
"The batting has probably let us down and the challenge when you've had a couple of poor batting performances is that people start to doubt their place in the team or their role in the team," he said.
"What we want is for our guys to have absolute clarity and bat the way we know they can bat."
New Zealand have injury issues of their own. Grant Elliott is missing again with a calf problem and former captain Daniel Vettori will face a fitness test on Wednesday morning after making his long-awaited comeback against Sri Lanka.
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