Mr Hofer is aiming to win a rerun of the presidential election on 2 October after his Freedom Party won a court challenge over voting irregularities.
After UK voters backed Brexit, he said Austria might also hold a referendum.
However, he has now made clear he thinks leaving would be a "mistake".
"I'm not in favour of an Austrian exit from the European Union; I've been annoyed for days that people have assumed I am," he told Die Presse newspaper (in German).
Mr Hofer was recently narrowly beaten by Alexander Van der Bellen, a Green Party-backed candidate, in a presidential election - but the vote was overturned a week ago after the Freedom Party (FPOe) argued that postal ballots were illegally handled in 94 out of 117 districts.
The far-right leader distanced himself from French National Front leader Marine le Pen, saying he did not share her clear anti-EU policy.
Mr Hofer's party hopes the rerun will boost his chances on 2 October, but the entire process has been overshadowed by the UK referendum vote to leave the EU.
Although latest polls give him a lead over Mr Van der Bellen, a Gallup poll of 600 Austrians suggested 60% opposed any referendum and only 30% favoured an "Oexit".
Another survey by the Austrian Society for European Politics suggested that only 23% wanted to leave the EU, a decline of eight percentage points since its last poll in late April and early May.
Mr Van der Bellen said on Thursday that his opponent and the FPOe were playing with fire if they "fantasised about an Austrian exit from the EU".
The far-right leader had appeared to back a referendum late last month when he said that Austrians should be given a vote "if within the next year the [EU's] course is towards centralisation".
But in his interview for Die Presse, Mr Hofer made clear he thought that leaving the EU would "undoubtedly be damaging" for Austria.
Leaving the EU would be a "last resort", he stressed, if Turkey joined the bloc or if there were new, centralised EU treaties.
Austria's outgoing president, Heinz Fischer, finally stood down on Friday after 12 years in office, leaving the country without a ceremonial head of state until late November at the earliest.
In his final address to parliament, he spoke of the UK's decision to leave the EU as "very regrettable and short-sighted".