The Marc VDS Honda rider has been diagnosed with hairline fractures to his T6 vertebra and a broken right wrist after suffering a high speed crash at Turn 8.
Miller was taken to the nearby Leoben hospital where his injuries were confirmed.
As result the Australian rider will be forced to miss a race for the second time this season after a foot injury ruled him out of the Circuit of Americas round in April.
The injury will come as a blow to the Assen race winner who entered this weekend's race fully fit for the first time this year.
The Townsville rider had previously suffered a broken leg following a motocross crash in pre-season.
Miller's latest injury will put him in doubt for next weekend's Czech Republic Grand Prix at Brno. A decision on his participation will be made on Wednesday.