An 18-year-old man previously stopped at Sydney Airport from flying to Syria has been arrested by counter-terrorism police for allegedly plotting an attack on home soil.

Tamim Khaja from Macquarie Park, in Sydney's north-west, was arrested on Tuesday morning with police alleging he was attempting to buy a gun and had scouted sites in Sydney for an "imminent" attack.

Police said Mr Khaja came to their attention last year, and was linked to others currently before the courts on terrorism offences but it will be alleged he was planning an attack alone.

"We are satisfied that any threat to the community posed by this individual has been mitigated," acting Deputy Commissioner of the Australian Federal Police Neil Gaughan said.

"We are satisfied that this individual was acting alone. We will allege that this individual was looking at possible sites in Sydney to undertake a terrorist attack and was making arrangements to acquire a firearm."

Mr Khaja was allegedly prevented from flying to Syria on three occasions, the most recent occurring in February when he subsequently had his passport cancelled. He then allegedly turned his attention to acquiring a weapon and planning his attack in Sydney.

Police would not specify which sites in Sydney the 18-year-old was alleged to have been targeting only that they were "institutions of authority".

He has been charged with two offences - allegedly planning a terrorism attack and preparation for foreign incursions and will appear in Parramatta Local Court on Tuesday afternoon. Both offences carry a maximum sentence of life imprisonment.

"We do have international obligations to stop these people from travelling offshore," Mr Gaughan said.

His arrest is not related to raids currently underway in Melbourne where offices are searching properties linked to five men charged over a plan to travel by boat to Indonesia in a bid to join Islamic State.

The Melbourne men were arrested last week north of Cairns, and properties linked to the group were raided on Tuesday morning.