The two men arrested at the weekend at a refugee centre in the western city of Salzburg "are not French, but are an Algerian and a Pakistani," the source said, asking not to be named.
Salzburg prosecutors had on Wednesday said the two had "arrived from the Middle East" with officials probing "indications of a possible link" to the November 13th Paris attacks.
The arrests reportedly came after a tip-off from French police and the source said that French investigators had travelled to Salzburg to question the men.
The Kronen Zeitung tabloid, which first reported the arrests, had said the two were French and were holding fake Syrian passports.
Officials in Austria and sources in France were on Wednesday unable to confirm this.
The paper said they arrived in October together with members of the cell behind the Paris attacks as part of the huge wave of migrants who have entered Austria from the Balkans this year.
Salah Abdeslam, the fugitive 26-year-old French citizen thought to have played a key logistical role in the attacks, was known to have been in Austria on September 9th.
According to the Austrian authorities, he was pulled over in a routine traffic check on his way from Hungary to Germany. With him in the car, which had Belgian number plates, were two unidentified men. They were all allowed to continue.
The Salzburger Nachrichten daily reported on Thursday that investigators have reconstructed Abdeslam's journey in his hired Mercedes thanks to the car's anti-theft tracking device.
The paper said he drove through Austria to the Hungarian-Serbian border, and was pulled over again on the return leg of the journey -- this time by police in the southern German state of Bavaria.
It said he picked up two men in Hungary -- Soufiane K. and Samir R. -- and that both had fake Belgian passports.
Hungarian officials said Abdeslam had travelled to Hungary before the attacks but did not say when.
Earlier this month, French sources said Abdeslam was in Hungary on September 17th, meaning he may have made several trips in the run-up to the attacks.
Three of the nine Paris attackers have yet to be identified, including two of three suicide bombers who blew themselves up outside the Stade de France stadium, who appear to have used fake passports to sneak into Europe.