The security presence comes as the Catholic Church continues to deal with the fallout from the announcement of a royal commission and a Victorian parliamentary inquiry into child abuse.
Victims' rights groups say the security tactic showed the church was putting the protection of property before the rights of the abused.
But the Archdiocese of Melbourne, which oversees St Patrick's, said the security guard was employed to make sure masses were not disrupted.
Mark Fabbro, of victims' group Survivors Network of Those Abused by Priests, was told to leave church grounds by the security guard for handing out flyers that asked victims to report their concerns to police.
Mr Fabbro said the security guard approached him when he began talking to parishioners.