Police say they have thwarted a "serious act of violence" after arresting 15 people and charging one in the wake of counter-terrorism raids across Sydney and Brisbane on Thursday.

But the Australian Federal Police and NSW police have refused to confirm media reports that the suspects were planning to snatch and behead a random member of the public.

NSW Police Commissioner Andrew Scipione refused to confirm the exact nature of the charges the suspect was facing but said details would be made clear when the person faced court in Sydney later on Thursday.

"The violence was to be perpetrated on a member of the public on the streets and certainly at this stage was at a very high level," he told reporters in Sydney.

But Commissioner Scipione called for the public to remain "calm".

"We don't need to whip this up," he said. "All of those plans that may have been afoot have been thwarted.

"Today's operation reflects the reality of the threat we actually face."

Commissioner Scipione said it was "of serious concern" that there were people in the "heart of our community" planning attacks, but said "we have in fact disrupted that particular attack".

Eight hundred police raided properties and cars in the Sydney suburbs of Beecroft, Bellavista, Guildford, Merrylands, Northmead, Wentworthville, Marsfield, Westmead, Castle Hill, Revesby, Bass Hill and Regents Park in what authorities say is the largest counter-terrorism operation in Australia's history.

Police used 25 search warrants to carry out the raids, which were ongoing on Thursday, and said three people tried to resist arrest. A firearm was seized, but Commissioner Scipione said it was "too early" to assume that would be the only weapon gathered.

Seventy AFP officers were involved in raids in Brisbane but AFP acting assistant commissioner Andrew Colvin said they were not necessarily linked.

"So while the raids in Queensland are not directly related to what's happened here today in NSW, the investigations continue and we are looking at linkages between the two," Mr Colvin said.

But Mr Colvin said Thursdy's raids were a "follow-up" to last week's arrests in Brisbane. 

NSW police are launching a new operation, in which 200 police will be sent to areas where attacks may occur.  "We won't be tolerating any misbehaviour on the streets," the NSW Police Commissioner warned.

Immigration Minister Scott Morrison said on Thursday that the scale of the operation "demonstrates the very real threat that's there, and the incredibly good work which is being done by the agencies".

He said the government was being strong in dealing with the threat both at home and abroad.

"I think this just demonstrates again that we are dealing with something that is very real here, the government knows that, we're responding accordingly," he said.