Sydney Anglican Archbishop Peter Jensen told his congregation atheism is not the rational philosophy that it claims to be.
Dr Jensen told the congregation that atheism is as much of a religion as Christianity.
"It's about our determination as human beings to have our own way, to make our own rules, to live our own lives, unfettered by the rule of God and the right of God to rule over us," he said.
"What we're really seeing, once more [is] an example of the contest between human beings and God over who rules the world."
The Anglican Archbishop's comments were mirrored by the Catholic Bishop of Parramatta, Anthony Fisher.
In his Easter address, he said Christianity has proved to be both vulnerable and hardy in the last century.
"Last century we tried godlessness on a grand scale and the effects were devastating: Nazism, Stalinism, Pol Pot-ery, mass murder, abortion and broken relationships - all promoted by state-imposed atheism," he said.
"[It's] the illusion that we can build a better life without God."
Atheist Foundation president David Nicholls says the comments are an act of desperation by the church.
"We're not forcing anything on anybody," he said.
"Hitler, who was a Catholic, forced Nazism onto the German population.
"Stalin forced his ideology onto the population. They didn't do any of these things in the name of atheism, in fact Stalin was trained in a seminary."
In his sermon, Dr Jensen said the passion of its followers shows atheism a religion in itself.
But Mr Nicholls says that atheism does not have its own belief structure.
"The passion and vigour that Peter Jensen refers to is only in his own mind," he said.
"Because atheists say it as it is, and it's against what Peter thinks, he would have to include those words.
"Atheism is just the acceptance that there is no God, and apart from that people make their own decisions."
The anti-atheist messages come after a global convention on atheism was held in Melbourne last month.
Organisers of the Rise of Atheism conference say about 2,500 people attended the event which included keynote speaker Richard Dawkins.
Cardinal Pell's message
Meanwhile, the leader of the Catholic Church in Australia, Cardinal George Pell, acknowledged that the Catholic Church has had a lot of negative publicity in recent years.
But he used his Easter address to remind Australians of the important work Christians do for the community.
Cardinal Pell says Christian teachings are the foundation of the Western way of life, including the Australian notion of a fair go.
"We often hear about Christian failures to live up to Christian standards and there have been too many scandals and many victims but the great majority of Christians continue to follow the commandments of love through regular service, tolerance, forgiveness and community building," he said.
"Australians believe that everyone is entitled to a fair go because of the Christian teaching that every person, unlike the animals, is made in God's image.
"Great efforts are made at a considerable expense to help the elderly, the sick, the unemployed, delinquent children, the marginal lives."
Anglican Church Primate, Archbishop Phillip Aspinall, urged people to think of stories of hope that emerge from natural disasters such as the Haiti earthquake.
Meanwhile, in pre-Easter celebrations in Rome, Pope Benedict celebrated Maundy Thursday mass at Saint John in Lateran Basilica.
He commemorated Christ's Last Supper by washing the feet of 12 priests representing the apostles, which is a symbol of humility.
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