The girl, whose name wasn't released, was arrested on Saturday evening at a Vienna railway station and remained in custody today.
The girl disappeared on Wednesday.
Police said her family believed she had been radicalised and feared she planned to join the Islamic State group in Syria.
Police spokesman Roman Hahslinger says there are no indications the teen planned any terrorist acts in Austria.
He says she denies wanting to go to Syria.
A decision is expected tomorrow whether to keep the suspect in Austrian investigative custody or turn her over to Swedish authorities.
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