Police spokesman Patrick Maierhofer told The Local that the 46-year-old widowed Turkish mother of the two sisters, Setaniye S., reported that her two daughters, Violetta (17) and Viktoria (16) left their home in Vienna at 11:30 pm on Saturday evening with just their passports.
She is worried that they may have attempted to travel to Syria to join Isis in its 'holy war', although Maierhofer said that so far there is no evidence that they had been radicalized.
The girls took no luggage, just their mobile phones, which have since been turned off. Police do not know if they had any money with them.
"Reviewing their behaviour over the last few weeks I'm convinced and worried that they may have travelled to Syria to join Isis and fight in the Jihad," the Kronen Zeitung newspaper quoted Setaniye as saying.
"They were acting a bit strange but as a single mother I was always busy, so perhaps I didn't pay as much attention as I should have."
She said that they had told her that they were going to buy cigarettes from a vending machine but when they failed to return an hour later she became worried and called the police.
"I lost my husband a year ago from cancer, and it hit the girls hard," she said.
"The two seemed to have been taking some comfort from religion but I was worried lately that they appeared to be getting a bit extreme."
Setaniye and her late husband left Turkey to live in Austria 20 years ago.
Earlier this year Samra Kesinovic, 17, and her friend Sabina Selimovic, 15, left Vienna to fight in Syria, a decision believed to be influenced by their recent radicalization through a local mosque.