Two men have been arrested on suspicion of terrorism offences, reports said.
Authorities said the men were "involved in recruiting, facilitating, and funding people to travel to Syria to engage in hostile activities".
Australia is working to stop people joining Middle East jihadist groups.
The two men, aged 21 and 31, were arrested at the iQraa Islamic Centre south of Brisbane.
Both would be charged with preparing for incursions into Syria, Australian reports said. The 21-year-old would be charged with recruiting fighters to join the conflict, while the 31-year-old would be charged with providing funds to militant group Jabhat al-Nusra.
The men were not suspected of planning attacks in Australia, a federal police spokesman said.
Witnesses said that police arrived early on Wednesday morning with a locksmith to access the centre, which sells books, gifts and clothing, according to Fairfax Media.
The Australian Broadcasting Corporation said police also raided a gym in the same area.
It reported that one of the centre's founders is believed to be the brother of Abu Asma al Australi, who is suspected of being the first Australian suicide bomber to die in Syria.
But an iQraa employee denied that the Islamic centre and the two men were linked to terrorism.
He told ABC that the arrests happened because of the authorities' "paranoia" and security concerns for the G20 summit, due to be held in Brisbane in November.
A customer also told the AAP that the two men were "born and bred" Australians and the centre is "harmless".
Authorities have previously said that 100 or more people in Australia were "actively supporting" militant groups fighting in the Middle East.
The raid took place a day after the head of the Australian Security and Intelligence Organisation, David Irvine, said he was assessing whether to raise the threat level.
Australia has been at "medium" since the threat level system was introduced in 2003, according to the country's national security website.
"Medium" means an attack could occur. It is followed by "high", which means an attack is likely and is the second highest threat level.
Mr Irvine told the ABC that the threat had been building in Australia over the past year and he had an "elevated level of concern".
He said this was due to "the numbers of people we are now having to be concerned about in Australia, because of the influence of Syria and Iraq on young Australians both in terms of going to those places to fight, but also in terms of what they are doing here in Australia with a potential intent to attack".
Officials have said that at least 60 Australians are believed to be fighting with jihadist groups in Syria and northern Iraq, and 15 Australians have been killed so far from those conflicts including two suicide bombers.
Australia has moved to restrict citizens from travelling to certain areas to join militant groups, and is in the midst of installing counter-terrorism units and biometric screening at all international airports.
Police in Australia have raided an Islamic centre in Queensland, a day after the country's spy chief said he was considering upgrading the terror threat level.