The pair, aged 18 and 20, are believed to have links with the Somali community and flew out of Sydney in the past fortnight after lying to their families about why they were travelling, News Corp Australia reported on Sunday.
While there have been cases of women joining husbands or boyfriends in the Syrian war zone, this is believed to be the first case of young women going there independently.
If the pair travel to the Islamic State group's stronghold in northern Syria they will face a jail term of up to 10 years if they return to Australia.
The IS group has issued a worldwide recruitment drive to secure brides for jihadists fighters.
Attorney General George Brandis would not comment on any individual cases but said families were now on the frontline of authorities hopes of stopping young Australians from travelling to the region.
'These terrorist organisations are taking advantage of vulnerable youths and luring them
on false pretences,' he told News Corp.