The paper said that the girls are currently in the Islamic State controlled city of Rakka in northern Syria, had been married to Chechen fighters upon their arrival in Syria and were both pregnant.
Spokesman for the Interior Ministry, Karl-Heinz Grundboeck, said however that decision may be too late.
He said: 'The main problem is about people coming back to Austria. Once they leave it is almost impossible.'
The news comes despite reports which surfaced last month that one of the girls may have been killed.
However, these reports were never officially confirmed and the Interior Ministry could not ascertain if they were correct.
The motivations of the two Bosnian girls are unclear but before leaving, they had contact with Chechen youths, and visited a mosque in Vienna's second district.
And police also expressed concerns that the pair were inspiring their contemporaries after two other teenage girls were caught attempting to flee the country to join IS ranks.
Little information was given about the copycat pair hoping to join Islamic State apart from the fact that one was 16 and the other was 14 and their parents were apparently from Iraq.
Police now want to find out how they became radicalised, and whether anybody had helped them plan their trip to Syria which was apparently set to take place via Turkey - following the same route as the other two girls.
The pair were caught when the mother of a third friend who was supposed to be travelling with them became suspicious about the amount of luggage her daughter was packing.
As many as 130 people from Austria are now believed to be fighting as jihadists abroad.
More than half of Austrian's jihadists originally come from the Caucasus region and have a valid residence permit in Austria.
.