The 31-year-old, named in local media as Phillip Galea, appeared in court after he was charged with planning or preparing for a terrorist act and collecting or making documents to facilitate an attack.
Galea told the Melbourne Magistrates’ Court he would fight the charges, adding that they were “a conspiracy against the patriot movement”.
Police would not confirm if he was a member of the anti-Islam Reclaim Australia group but said he had a “number of affiliations to different organisations”.
There were violent clashes between left and right-wing groups over immigration in Australia’s second-largest city in May and June, sparking a push by the Victoria state government to boost police powers.
Victoria state premier Daniel Andrews said Sunday there was “no imminent threat” after the weekend police raids but that authorities remained vigilant.
Anti-Muslim sentiment has mounted in Australia in recent years after a series of attacks by radicalised youth, including the killing of a police employee in Sydney in October.
The Joint Counter-Terrorism Team, which took part in the operation on Saturday, has been carrying out a series of raids in various cities amid increasing concern about home-grown extremism.
Canberra raised the terror threat alert level to high in September 2014, while parliament has passed a suite of new national security laws.