Wilders, a right-wing Dutch MP, made a speech in Melbourne on Tuesday in which he warned Australia could have a grim future under Islamic law and urged an end to the building of mosques across the country.
He said Europe's capitals were being changed by mass migration from Islamic countries and warned the same thing could happen to Australia.
Wilders' views have been widely condemned but Senator Bernardi says his visit underlines a "double standard" when it comes to free speech in Australia.
In a blog post on Wednesday, Senator Bernardi points to reports that Jews and gay people in the Netherlands no longer feel safe from attack by Islamic fundamentalists.
"These fundamentalists are the same people who want to kill Wilders and establish sharia law under a global Caliphate because Muhammad commanded them to back in the 7th century," Senator Bernardi writes.
"And yet, it is Wilders who is characterised as an extremist."
Senator Bernardi also questions why it was so hard for Wilders to get an Australian visa but hardline Muslims like Hizb ut-Tahrir leader Taji Mustafa seem to have no issues.
Senator Bernardi says it does not matter whether people agree with Wilders.
"What is important is that we are prepared to stick up for free speech even if we don't like what we hear," he says.
"The double standard that the government and parts of the media have in relation to freedom of speech and what is acceptable for public debate is simply unacceptable."
Opposition Leader Tony Abbott said Mr Wilders' comments on Islam were substantially wrong but that he was entitled to his viewpoint.