Wednesday's raid on al-Furqan center came on the second day of a joint counter-terrorism operation by Victoria police and Australian Federal Police, the Australian Broadcasting Corp. reported.
Adnan Karabegovic, 23, was arrested in the raid and charged with four counts of collecting a document connected with the preparation for engagement in a terrorist act.
Imam Ibrahim Omerdic of the Bosnia and Herzegovina Mosque called for federal police to apologize for the raid. The agency's publicity on the operation painted a dark picture of Islam, he said.
The operation did not target racial or religious communities, Police Minister Peter Ryan said.
Omerdic said the center was a fringe group and did not represent the Islamic community.
Ramzi el-Sayed, president of the Islamic Council of Victoria, said he had been notified by police about the raids Wednesday afternoon and was on alert for any backlash against the city's Muslims.
Little is known about the center where the raid took place, el-Sayed said. The center is not a member of established Islamic organizations, and neither the center's leader nor its members are involved in the larger community.