Norbert Hofer of the Freedom Party (FPOe) won 36.7 of the vote, projections showed, with candidates from the two governing parties failing to even make it into a runoff on May 22, projections showed.
The result, if confirmed, means that for the first time since 1945, Austria will not have a president backed by either the Social Democrats (SPOe) or their centre-right coalition partners the People's Party (OeVP).
The SPOe's candidate Rudolf Hundstorfer came joint fourth with just 11.2 per cent, level with Andreas Khol of the OeVP.
Facing Hofer on May 22 will instead be either Alexander van der Bellen, backed by the Greens, who garnered 19.7 per cent, or independent candidate Irmgard Griss, a former judge hoping to be Austria's first female president, who won 18.8 per cent.
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The only candidate who fared worse than the main parties' candidates was Richard Lugner, an 83-year-old construction magnate and socialite married to a former Playboy model 57 years his junior, who won 2.4 per cent.
"Like elsewhere in Europe, we are witnessing the downfall of the traditional parties," political analyst Peter Hajek told AFP.
Leading opinion polls ahead of 2018 general elections with more than 30 per cent is the FPOe, boosted by Europe's migrant crisis despite a firmer line in recent months from Chancellor Werner Faymann's government.
Austria no longer has the lowest unemployment rate in the European Union and Faymann's coalition, in power since 2008, has bickered over structural reforms.
Heads could roll in the current government if neither candidate makes it into the run-off, she said before the results were announced.