"We are investigating because of the suspicion of breach of trust and corruption," the public prosecution office for economic and corruption affairs (WKStA) said.
The $100,000 (€84,000) transfer was made by Fifa, the world governing body, to a project supporting young footballers in Africa at the beginning of 2015.
The patron of this project was none other than the wife of the head of the Austrian Football Federation (ÖFB), Leo Windtner.
According to two Austrian websites, Addendum and 90minuten.at, the funds were approved just after Windtner had said in an interview that he supported Blatter serving another term.
The money was initially wired to the ÖFB, which returned it to Fifa, saying it was not involved in the African project. Fifa then transferred it directly to the project's account.
Windtner, 67, said on Wednesday that he would make a statement to prosecutors in the coming days and that he was "relaxed" about the probe.
"I didn't give Blatter any promise or undertaking," Windtner said. "Everything was transparent and every cent accounted for. I have nothing to reproach myself for."
He conceded that the money was at first wrongly transferred to the ÖFB and not to the African project, "but that was no fault of mine".
In the end, the ÖFB supported Blatter's rival for the Fifa presidency, Prince Ali bin al-Hussein of Jordan.
Blatter won re-election but amid swirling corruption allegations the Swiss was later banned from soccer for making an improper payment to then-Uefa chief Michel Platini.