ASIC said clients should "urgently review" their accounts, including transaction history and change passwords.
It said it became aware of the breach during "regular surveillance" of local financial markets.
Clients should update anti-virus signatures and report fraudulent transactions to stockbrokers.
ASIC said it was working with stockbrokers to assist victims.
"ASIC is also working with other authorities to identify the source of the intrusions and pursuing a line of enquiry consistent with similar incidents in overseas markets," it said in a statement.