Michael Clarke's desperation to play for Phillip Hughes in the first Test has resulted in another flare-up of the captain's chronic back condition and left his immediate future uncertain.

There were countless reasons why Clarke should have played in Adelaide but the big reason why he should have sat out was dramatically laid bare about 25 minutes before tea on Tuesday.

Sad walk off: Michael Clarke leaves the Adelaide Oval after injuring his back. Photo: Getty Images

Clarke had pleaded with selectors last month to take him on trust with his fitness but they will be reluctant to do so again.

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The seriousness of Clarke's problem is not yet known but given his long injury history with back and hamstring issues any recurrence is of great concern. Clarke had injections in his lower back on Tuesday night and will be monitored in the morning.

"We'll have to wait and see but it didn't look too good out there," David Warner said.

The innocuous circumstances leading to his latest setback further highlighted the 33-year-old's increasing vulnerability to injury.

His availability for the rest of the series is now in grave doubt and there could be implications for Australia's World Cup preparations.

Clarke was set to be ruled out of the first Test last month but Hughes' death forced a change in Cricket Australia's priorities.

Selectors had wanted Clarke to prove his fitness in a warm-up game but after the recent extraordinary events they respected his wish to play.

CA chief James Sutherland, who was appearing as a guest on the ABC's broadcast when Clarke broke down, said the skipper's disagreement with selectors was now a "moot point".

"Everyone was working together with the same thing in mind to try to get Michael recovered and fit and ready to play," Sutherland said.

"There may well have been some slightly different views about what was best in terms of preparation, but really that's all a moot point now.

"Things have moved on, we've seen the extraordinary and tragic circumstances of Phillip's death and we hope Michael's OK and he's back on the ground very soon. 

"It's always a worrying sign when the Australian captain's carrying any sort of injury. We'll leave it in the capable hands of [physiotherapist] Alex Kountouris and he can weave a bit of magic overnight perhaps."

For the first half of the day the move to play Clarke appeared a winner. Inspired by his off-field leadership and his effort to be fit, Australia batted into a position of dominance thanks to a stirring century from David Warner.

Clarke appeared destined to follow with a ton of his own in Hughes' honour before the fears of CA's medical team were realised.

An odd hush fell across Adelaide Oval when Clarke dropped to his knees grimacing in pain after twisting slightly to avoid a harmless bouncer from Ishant Sharma. The ball was so short there was never any danger to Clarke's head.

Clarke then lay on his stomach to stretch out his back but was in noticeable discomfort.

He received treatment from team doctor Peter Brukner and Kountouris but it was quickly decided that Clarke was not fit enough to continue his innings. He retired hurt on 60.

Clarke cut a dejected figure as he trudged gingerly off the field, the warm ovation he was receiving from the crowd unable to lift his spirits.

The reaction of his wife Kyly, who had her hands on her head in disbelief, summed up the crowd's shock.

Clarke left the ground soon after to seek further treatment and was in "considerable pain", Cricket Australia said.

With batsmen no longer allowed runners, Clarke may not be able to bat again this game unless his discomfort dissipates.

The setback comes less than four weeks after he suffered his third hamstring strain in as many months, and seventh of his career, in Perth.

Clarke's back and hamstring injuries are intertwined. His back problems put extra pressure on his hamstrings.

Kountouris had said last month that the danger of another relapse was ever present.

"That's our biggest fear, isn't it? Once he's done it once, twice, the risks go up of a recurrence," Kountouris said.