About 15 victims and representatives of victims of clergy sexual abuse protested outside the cathedral as well as around 100 members of a Campbellfield church demanding the reinstatement of their former priest.
The rallies come as Pope Benedict XVI prepares to visit Sydney during celebrations to mark World Youth Day.
In Good Faith and Associates (IGFA) spokeswoman Helen Last said victims want restorative meetings.
"The Pope has promised there will be a big pastoral engagement and we're not seeing any of it and haven't seen any of it for 10 years," Ms Last said.
Members of the group will head to Sydney during the Pope's visit, but are concerned about "draconian" laws introduced by the NSW government which have been criticised for impinging on free speech.
Ms Last met with NSW police to discuss the laws last week and was informed any clothing or banners needed to be approved.
The group has produced t-shirts saying "bloody angry Aussies against clergy sexual abuse".
"These are the most draconian laws that have ever been brought in and I think they say something about the unsavoury and unhappy relationship between the church and the state and that needs to be sorted out," Ms Last said.
A spokesman for Archbishop Hart said he had no plans to meet victims of clergy sexual abuse.
Members the Our Lady Guardian of Plants church in Campbellfield in Melbourne's north east demanded their former priest Father Khalid Marogi be reinstated at the parish.
About 50 protesters stormed St Patrick's for about 15 minutes, disrupting mass with loud chanting, until police asked them to leave.
Spokesman Robert Yacoub said Fr Marogi was removed from the church without any warning.
The church is of the Chaldean arm of the faith with 10,000 Iraqi parishoners.
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