The Kronen Zeitung newspaper reported that the pair are French citizens posing as refugees, who travelled with some of the Paris attackers through Greece and the Balkans in early October, using fake Syrian passports.
They were arrested over the weekend after police received a tip-off from a foreign intelligence service. There is some speculation that they were waiting in Salzburg for orders to carry out further terrorist attacks.
A spokesman for the state prosecutor, Robert Holzleitner, said he cannot confirm if they planned to carry out terror attacks and declined to comment on their nationalities, saying that they had "come from the Middle East".
He did confirm that "indications of a possible link to the Paris attacks are currently being investigated".
In a related story, two asylum seekers suspected of being members of the Isis terror group were taken into custody in Salzburg just a few weeks ago.
The pair, aged 20 and 21, are reported to have boasted to other refugees and volunteers that they had fought with Isis in Syria.
Prosecutors have said that so far there is no evidence that they planned to carry out attacks in Europe or that they had any links to previous attacks.
Salah Abdeslam, a 26-year-old French citizen who is thought to have played a key logistical role in the Paris attacks, is still on the run and subject to an international arrest warrant.
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Abdeslam was also registered as having been in Austria on September 9th after being stopped in a routine traffic check in a car with Belgian number plates with two other men, Austrian authorities said on November 17th. Abdeslam told police he was "on holiday" in Austria.
He also travelled to Hungary before the attacks where he "recruited a team" from unregistered migrants passing through, Hungarian officials said on December 3rd.