Cardinal Pell made the comments to Catholic politicians in his regular Sunday Telegraph column at the weekend.
"The Catholic Church is not a duty-free assembly of free-thinkers. Neither is it a group of people who loyally follow their conscience. Every person has to do that," he wrote.
Premier Morris Iemma and his deputy, John Watkins, were among Catholics who voted for the legislation.
When Mr Iemma was asked yesterday whether he would attend Mass and receive Communion this weekend, he said it would depend on the storms.
"I will do what I do and that is I will go to church and I intend to take Communion," he said.
"Now, tomorrow depends on what else happens with these extraordinary storms and the damage that has been caused."
Dr Pell said all Catholics who rejected the Church's teachings should not be "comforted" for their views.
"Catholics are not created by the accident of birth to remain only because their tribe has an interesting history," he said.
"All Catholics who continue to reject important Catholic teachings, even in areas such as sexuality, family, marriage, abortion, euthanasia, cloning where 'liberals' claim the primacy of conscience rules, should expect to be confronted, gently and consistently, rather than comforted and encouraged in their wrongdoing."
Similar remarks made by the Catholic Archbishop of Perth, Barry Hickey, were referred to that state's parliamentary privileges committee after the Speaker said that they were "threatening" to MPs.
Pell entitled to view, constitutional lawyer says
But Mr Iemma said he did not believe Cardinal Pell had overstepped the mark.
"I don't believe that he has," he said. "The cardinal is entitled to his view."
Constitutional expert George Williams said yesterday he believed George Pell had acted within his rights.
"George Pell and others are as entitled as environmentalists to put their point of view to encourage or persuade people to vote a certain way,'' he said.
"They are entitled to put arguments based on religion, common sense or law."
The dispute has split Catholics, with high-profile Jesuit Frank Brennan last week insisting every Catholic was required to act according to conscience.
The Sydney Morning Herald reports that several Catholic MPs including the Deputy Premier, John Watkins, and the Nationals' Adrian Piccoli, ignored warnings from the Archbishop of Sydney, George Pell, and received Communion at Mass yesterday.
Mr Watkins and Mr Piccoli last week voted to support embryonic stem cell research despite Cardinal Pell warning they faced "consequences" in their religious lives for supporting the research.
Cardinal George Pell, Question of conscience (Sunday Telegraph, 10/6/07)
MPs abstain from communion: Pell (Sunday Telegraph, 11/6/07)
Pell ignored as MPs take Communion (Sydney Morning Herald, 11/6/07)
Faithful in lock step behind the cardinal (Sydney Morning Herald, 11/6/07)
LINKS (not necessarily endorsed by Church Resources)
Archdiocese of Sydney
George Pell (Wikipedia)
WA parliament may reprimand Hickey (CathNews, 8/6/07)
Anglicans, Baptists back Pell (CathNews, 8/6/07)
Coast to coast controversy over stem cell vote (CathNews, 7/6/07)
Catholic pols defy stem cell communion threat (CathNews, 6/6/07)
Pell slams "open slather" for stem cell research (CathNews, 5/6/07)
Life office slams human "sub-class" Vic cloning law (CathNews, 11/5/07)
Hart confronts Bracks over cloning legislation (CathNews, 12/4/07)
Bracks defies Pope on cloning (CathNews, 19/3/07)
Archbishop Hart condemns cloning laws (CathNews, 14/3/07)
Christianity not driver in cloning vote: Garrett (CathNews, 19/12/06)
Christian opposition fails to stop cloning bill passage (CathNews, 7/12/06)
Late amendment puts cloning bill passage in doubt (CathNews, 6/12/06)
Premiers face stem cell backlash as Hart criticises debate (CathNews, 24/7/06)
Catholics divided over stem cells (CathNews, 14/7/06)
Don't lift ban on cloning, says Brennan (CathNews, 23/6/06)
12 Jun 2007