Justice minister Michael Keenan said the agency would focus on stopping money flowing through Australian financial institutions, as well as helping banks in the region improve their own protections.
“The need for greater cooperation with our neighbours has never been more critical,” Mr Keenan said.
He warned of the need to “stamp out” IS efforts to establish a presence in Asia.
Another two Australian Federal Police officers will arrive in the Philippines by the end of September, joining the four already there.
Australia is already providing military assistance to the Philippines, which has been battling an IS-linked insurgency in the city of Marawi since May.
Australian P3 Orion spy planes have conducted surveillance flights over Marawi and given the information to the Philippines.
Australian and international officials have warned more jihadis may travel to South East Asia as the Islamic State group loses more territory in Iraq and Syria.
Mr Keenan’s office said AUSTRAC would be using “non-traditional approaches” to identify IS funding methods and shut them down.
