The Dutch TT winner had a high-speed crash at Turn 8 exiting the infield section and, having been thrown through the gravel trap, was diagnosed with hairline fractures to his T6 vertebra and right wrist at the nearby Leoben hospital.
He is also in doubt for next weekend's Czech Grand Prix at Brno, with Marc VDS saying checks on Wednesday would determine his participation.
The team tweeted: "Obviously, as he's as tough as nails, @jackmilleraus wanted to race today, but accepted the decision of the circuit medical team."
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It was Miller's third fall of the weekend, and he was due to start 20th.
Miller headed to Austria saying it was the first grand prix of 2016 that he had been at full fitness, having broken the tibia and fibula in his right leg in a motocross training fall in February.
It is the second race the Australian has missed this year, after being forced out of the Austin event in April when he reinjured his right leg in a Friday practice accident.
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