Officers arrested one man on Friday following raids at four properties in Sydney's southwest that police said were "part of a long-running investigation and not as a result of any specific terrorism threat".
The 33-year-old was arrested and charged with acquiring and possessing ammunition illegally, police said.
The investigation, which has been running for more than a year, is looking into alleged financial and other support for foreign fighters in conflicts including those in Syria and Iraq.
Police said the raids were not connected to the 16-hour standoff at a Sydney cafe in mid-December that left the lone gunman, self-styled Islamic cleric Man Haron Monis, and two hostages dead.
But they follow large-scale counter-terrorism raids across the country in September that came as Australia upgraded its terror threat to high on growing concern about militants returning from conflicts in the Middle East.
Separately, a 21-year-old man was arrested on warrants related to the possession of unauthorised and unregistered firearms and ammunition found in a separate raid last month.
His arrest came as part of an ongoing counter-terrorism operation into people suspected of involvement in domestic terrorist acts, fighting in Syria and Iraq and the funding of terror groups, police said.
Both men's cases were adjourned today until next week and lawyer Adam Houda, who is representing both men, stressed that his clients were not facing terror charges.
"There is no suggestion at all there is any links with any terrorism," he said outside court.
"One of the hallmarks of our justice system is the presumption of innocence. So presume them innocent."
The Australian government has said that more than 70 Australians are currently fighting for Islamist militants in Iraq and Syria, with at least 20 believed to have died.
Last year, Canberra passed a law criminalising travel to terror hotspots without good reason. Those charged could face up to 10 years in jail.

Latest News from World News Desk