Andreas Moelzer of the Freedom Party (FPOe) made the move after Austria's President Heinz Fischer urged him to pull out of the election altogether.
But Mr Moelzer, a serving MEP, has not withdrawn from the FPOe candidate list.
He has been widely criticised for calling the 28-nation European Union a "conglomerate of Negroes".
Austrian Chancellor Werner Faymann on Tuesday added his voice to those calling for Mr Moelzer to quit the election.
"Such a person should not represent Austria in the European Parliament," he said.
Mr Moelzer had also said the EU made Hitler's Third Reich look "informal and liberal". He has apologised for his comments.
Anti-establishmentOpinion polls put national support for the anti-immigrant FPOe at around 20%.
Explaining his decision, Mr Moelzer said "it is the evident loss of confidence in my party which is prompting me to do this".
He insisted that he was not responding to "the continuous pressure from the country's entire politically correct media or the hypocritical indignation of the republic's political establishment", the Austrian broadcaster ORF reported.
He also accused the "far left" of organising a "witch-hunt" against him.
'Out of place'Earlier, President Fischer called on him to step down, in an interview with an Austrian newspaper.
He said Mr Moelzer's views were "out of place in the European Parliament".
![Austrian president Heinz Fischer](http://news.bbcimg.co.uk/media/images/74098000/jpg/_74098617_74098616.jpg)
The Freedom Party's leader, Heinz-Christian Strache, has also distanced himself from Mr Moelzer. The two politicians had a meeting on Monday evening.
"Everybody in the FPOe community has to pay particular attention to the vocabulary they use," Mr Strache said.
In recent months the Eurosceptic Freedom Party has outscored Austria's governing Social Democrats and Conservatives in opinion polls, the BBC's Bethany Bell reports from the capital, Vienna.
It is now considered the main opposition party in Austria.
Last week the FPOe joined with France's National Front, Belgium's Vlaams Belang and the Sweden Democrats to form a new coalition, the Young European Alliance for Hope (YEAH).
But Mr Moelzer's remarks have attracted criticism from some of the European populist parties.
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