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In a dramatically blunt interview with an Italian Jesuit monthly, Francis said the Church had locked itself up in "small things, in small-minded rules".
Its priests, he said, should be more welcoming and not cold, dogmatic bureaucrats stuck in confessionals that sometimes resembled "torture chambers."
Francis, the first non-European pope in 1,300 years, the first from Latin America and the first Jesuit pope, did not hold out the prospect of any changes soon to such moral teachings.
But, in the 12,000-word interview with Civilta Cattolica, he said the Church must find a new balance between upholding rules and demonstrating mercy. "Otherwise even the moral edifice of the Church is likely to fall like a house of cards..."
His comments were welcomed by liberal Catholics; but they are likely to be viewed with concern by conservatives who have already expressed concern over Francis's failure to address the issues stressed by his predecessor, Benedict.
In the interview with the magazine's director, Jesuit Father Antonio Spadaro, he also said he envisioned a greater role for women in the 1.2 billion member Church but suggested it would not include a change in the current ban on a female priesthood.
In a remarkable change from his predecessor Benedict, who said homosexuality was an intrinsic disorder, Francis said that when homosexuals told him they were always condemned by the Church and felt "socially wounded", he told them "the Church does not want to do this".
He re-stated his comments first made on the plane returning from Brazil in July that he was not in a position to judge gays who are of good will and in search of God.
In the interview released on Thursday, he added: "By saying this, I said what the catechism says. Religion has the right to express its opinion in the service of the people, but God in creation has set us free. It is not possible to interfere spiritually in the life of a person."
The Church, he said, should see itself as "a field hospital after a battle" and try to heal the larger wounds of society and not be "obsessed with the transmission of a disjointed multitude of doctrines to be imposed insistently."
Francis' approach contrasts starkly with his conservative predecessor Benedict, who stepped down in February.
The interview was not didactic and formal, such as those of past popes, but easy-going, familiar and friendly. He even spoke of his favourite author, Dostoevsky), painter, Caravaggio and composer, Mozart.
John Gehring, Catholic program director at Faith in Public Life, a liberal advocacy group in the United States, said:
"This pope is rescuing the Church from those who think that condemning gay people and opposing contraception define what it means to be a real Catholic.
"Francis is putting a message of mercy, justice and humility back at the center of the church's mission. It's a remarkable and refreshing change."
The interview took place over three sessions in August in his simple quarters in a Vatican guest house where he has lived since his election instead of the spacious papal apartments, and was released simultaneously in translations by Jesuit journals around the world.
"We cannot insist only on issues related to abortion, gay marriage and the use of contraceptive methods. This is not possible. I have not spoken much about these things, and I was reprimanded for that," he said.
Just last week, Bishop Thomas J. Tobin of Providence, Rhode Island, spoke for many conservative Catholics when he said he was disappointed that the pope had not addressed "the evil of abortion" more directly in order to encourage anti-abortion activists.
Francis stressed that while not tampering with Church teachings, he suggested the Church had many other things to concern itself with.
"But when we speak about these issues, we have to talk about them in a context. The teaching of the Church, for that matter, is clear and I am a son of the Church, but it is not necessary to talk about these issues all the time," he said.
Speaking specifically of homosexuals, he said:
"We must always consider the person. Here we enter into the mystery of the human being. In life, God accompanies persons, and we must accompany them, starting from their situation. It is necessary to accompany them with mercy. When that happens, the Holy Spirit inspires the priest to say the right thing."
The Catholic Church teaches that homosexual tendencies are not sinful but homosexual acts are.
In several parts of the interview he stressed the need for mercy and understanding by priests.
"The confessional is not a torture chamber, but the place in which the Lord's mercy motivates us to do better," he said.
The pope also spoke about the role of women in the Church, saying their "deep questions must be addressed".
"We must therefore investigate further the role of women in the Church. We have to work harder to develop a profound theology of the woman. Only by making this step will it be possible to better reflect on their function within the Church," he said.
He hinted that he was open to giving women greater decision-making roles in the Church.
"The feminine genius is needed wherever we make important decisions. The challenge today is this: to think about the specific place of women also in those places where the authority of the Church is exercised for various areas of the Church," he said.
The Church teaches that woman cannot become priests because Jesus willingly chose only men as his apostles. Proponents of a female priesthood say he was only acting according to the norms of his times.