The government says it is the first time federal anti-terrorism laws are being used on a person allegedly holding what it calls "right-wing extremist" views.
Officers of the Victorian Joint Counter-Terrorism Team arrested the 31-year-old from the suburb of Braybrook during raids in Melbourne and regional areas on Saturday.
The Australian Federal Police are not revealing the substance of the charges against the man.
They say the targets of his allegedly planned attack may become clearer once he returns to court on August 9.
Federal police say his actions posed a potential threat to individuals in Victoria and may have resulted in damage to property.
Acting Assistant Commissioner Jennifer Hirst says two terrorism-related charges are being brought against the accused.
"We'll allege the 31-year-old man is a political extremist. His criminal actions included collecting or making documents that were likely to be used to facilitate a terrorist act and conducting activities that constituted planning for a terrorist act. There is no current or imminent threat to the community. We believe any threat that may have been posed by this man as a consequence of his actions have been appropriately mitigated."
Identified as Phillip Galea, the accused did not seek bail while appearing in Melbourne Magistrates Court on Sunday and remains in custody.
Mr Galea told the judge he would fight the charges and said they are part of a conspiracy against what he called "the patriot movement."
Federal police assistant commissioner Ross Guenther has addressed that claim.
"There's not a conspiracy around the patriot movement. This is purely part of an ongoing investigation we've had in play for some time where our concerns were very much that an individual's or group actions could lead to significant harm in this state. And I think, to that end, the Australian Federal Police and Victorian police will work very effectively with the security agencies to stop or mitigate that threat."
Federal justice minister Michael Keenan says the case has turned the attention of national anti-terrorism laws to what he calls alleged "right-wing extremism."
"This is the first time in the history of Australia that we have used Commonwealth terrorism laws to charge someone who is alleged to have been a right-wing extremist. This underlies the fact that, in Australia, we police the laws regardless of people's background, regardless of people's ideology. If somebody is a violent extremist and they present a threat to the Australian community, the police will take action."
Police have not confirmed the accused's affiliation with any particular group, although Mr Galea is reported to have links to the so-called True Blue Crew and Reclaim Australia.
Followers of both groups are known to promote views opposing immigration, the Muslim faith and multiculturalism.
Reclaim Australia co-founder John Oliver says Phillip Galea is not a member of his group but has had some contact with it.
"Well, he contacted us and wanted to help with the second Melbourne Reclaim Australia rally that we held in Melton, and we passed his number on to the organisers down there, and they accepted his help. And he was supposed to show up on the day at the Melton rally, but, obviously, two days beforehand, he was arrested."
The Australian Federal Police say warrants which were the basis of the weekend searches concerned other persons of interest as well.
They say it is possible more charges will be brought against other people.
