The alleged ringleader of a criminal network that sends Australians to fight in Syria has been arrested, the Associated Press reported.

Police estimate that about 100 Australian residents and citizens have travelled to Syria to fight in the civil war, some taking up arms with terrorist-linked militias.

Australian Federal Police deputy commissioner Peter Drennan said two Sydney men were the first suspects to be arrested in a four-month-old joint federal and state police counter-terrorism investigation.

"We will allege that one of the men is responsible for organising travel, arranging overseas contacts and facilitating travel into Syria for Australian citizens to fight on the front line," he said.

The 39-year-old suspected ringleader and a 23-year-old alleged recruit are due to appear in Sydney courts charged under the Crimes (Foreign Incursions and Recruitment) Act. The act outlaws Australian residents or citizens travelling overseas to fight or recruiting others to fight. It carries a maximum 10-year prison sentence.

New South Wales deputy police commissioner Catherine Burn said the network had already sent six Australians to Syria to fight.

"We have identified who we believe is the principal person involved in the facilitation network of sending people over to Syria to engage in conflict," she said.

Drennan said the difficulty in gathering evidence from Syria had prevented police making more arrests.

The Syrian war has attracted Australian civilian combatants like no other conflict in recent decades. Many are from Lebanese backgrounds.

Security chiefs fear many will become radicalised by the war and could pose a terrorist threat when they return to Australia.