Downer's Indonesian counterpart, Hassan Wirajuda, called on delegates to increase regional co-operation in the fight against such groups as Jemaah Islamiyah, blamed for the 2002 Bali nightclub bombings and a series of other attacks.
"We owe it to our citizens to wage an effective battle against terrorism," Wirajuda said.
He said greater co-operation between security forces in South-East Asia was needed to "counter the clever and seductive propaganda of the terrorists".
Indonesia has arrested and prosecuted almost 200 people for direct or supporting roles in attacks on its soil.
But one senior Indonesian official, speaking on the sidelines of the conference, said a particular problem in Indonesia lay with how the authorities handled those who had been convicted.
General Ansyad Mbai, head of counter-terrorism at the security ministry, said that many people who had been jailed for terrorist offences often emerged more organised and committed to violence than before.
Convicts, he said, were allowed to mix together in jail with leaders able to give instruction to other terrorists as well as common criminals.
He noted a recent case in which Indonesian police seized a laptop computer from one convicted terrorist leader who they said used it to communicate with sympathisers outside the prison.
"The prisoners should be treated specially - they should be split up from one another," Mbai said.
"We must not allow them to become united, stronger and more radical while they are in jail."