"Slander, indeed lying accusations against someone without any substance, have no place in public debate," Van der Bellen said.
In comments to online news outlets, the liberal ecologist targeted FPOe chief Heinz-Christian Strache who has made a series of controversial statements aimed particularly at the public broadcaster.
Strache, who is deputy chancellor, posted a photo on social media of a star newsreader with the caption, "There's a place where lies become news - it's the ORF", (Austrian Broadcasting Corporation).
Under fire over the post, Strache said it was "satire".
But Van der Bellen added: "Freedom of expression, freedom of the press and the independence of the media are indispensable conditions for dynamic liberal democracy, just as is the possibility of critical comments towards politicians."
The state television has long been a target of the far right which considers it beholden to traditional social-democrat and conservative parties.
It was the third time since the start of the year that the head of state has intervened to try to keep the FPOe in line.
The Freedom Party announced Tuesday a bid to clean up its pro-Nazi image by appointing a committee of historians to look into its history.