Authorities have said that the boy was allegedly planning to travel to Syria, and was considering building a bomb, with Vienna's Westbahnhof railway station one of several potential targets.
"He admitted he had plans to go to Syria and searched the internet for plans on how to build explosive devices," said Michaela Obenaus, spokeswoman for prosecutors in St. Pölten, the capital of the province of Lower Austria. "There is suspicion of participation in a terrorist organization."
According to Obenaus, the boy had "expressed sympathy" with Isis militants fighting in Iraq and Syria.
Justice officials have two days to decide whether 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. On Wednesday afternoon, the regional court in St. Pölten accepted a request by the prosecutor for the imposition of pre-trial detention.