Merkan G., a boy of Turkish origin who planned to commit a terrorist attack on the Westbahnhof railway station went missing on Tuesday afternoon.
The teenage jihadist who faced pre-trial detention in a remand home in Hütteldorf had planned to find crowds to maximize death in his bomb plans.
Authorities have said that the boy was allegedly planning to travel to Syria to join the Isis terror group, and was considering building a bomb, with Vienna's Westbahnhof railway station one of several potential targets.
According to Obenaus, the boy had "expressed sympathy" with Isis militants fighting in Iraq and Syria.
Justice officials decided in October to extend the boy's detention by a further two weeks, to allow additional investigations. In Austria, young people are considered criminally culpable from the age of 14.
Police in St. Pölten revealed that they had been investigating the boy since the beginning of October, since he had been making extremist statements and engaging in increasingly radicalized behaviours. In October, the regional court in St. Pölten accepted a request by the prosecutor for the imposition of pre-trial detention.