"There is no doubt the problem in Syria is one that we have been paying a lot of attention to over the last couple of years as you see jihadists coming in from Europe and as far as Australia to get trained and then going back into their home countries," Obama told CNN.
Australians are known to be fighting with al-Qaeda-linked groups, and with Isis, the Islamic State of Iraq and al-Sham, rapidly gaining ground in Iraq and accused of mass murder and brutality.
Isis, described as one of the world's most deadly and active terrorist organisations, is outlawed in Australia.
Attorney-General George Brandis said this sent a strong message to potential jihadists, who could face up to 25 years in jail on their return home.
While surveillance has increased and a number of passports have been cancelled, many still slip through the net.
Khaled Sharrouf, jailed for four years after being convicted in Sydney on terrorism-related charges, used his brother's passport to evade authorities to join Isis in Iraq.
Others have appeared in Isis online recruiting videos, urging Australians to join the fight. The fear is that they will bring the war home with them.
Australia has already uncovered a number of home-grown terrorists, including two cells planning attacks in Melbourne and Sydney.
Describing jihadists as trained killers who hated Australia's way of life, Prime Minister Tony Abbott said the Government would do everything humanly possible to prevent their return to the country.