Past president of the Ballarat Islamic Society, Ibrahim Sultan, said the people arrested on Thursday were "criminals who belong to no religion".
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"How anyone can think of such plans is beyond me and to be honest I'm not sure what this will mean for the Islamic community from now on."
Dr Sultan said Muslims were already "stared at" and "made to feel awkward", with the arrests on Thursday sure to heighten such views.
Hundreds of police made arrests in Sydney and Brisbane on Thursday, thwarting alleged plans to capture a random member of the public, kill them and drape the ISIL flag over their body.
"We are a peaceful people and this type of crime, or criminals, should not be associated with us," Dr Sultan said.
