"It really pains me when I come across people who no longer go to confession because they get harangued, badly treated, told off," Francis said in his homily at the ordination mass in St Peter's Basilica.
"They feel the doors of the church are being shut in their faces. Please don't do this. Have mercy," the Argentine pontiff said, adding: "It is not you who are the masters of doctrine, it's the Lord's doctrine".
Pope Francis has put forward a more tolerant and pastoral approach than his predecessors, insisting for example that priests should baptise the children of unmarried Catholic couples and single mothers.
He has also said the Catholic Church should not be "obsessed" with topics like abortion, contraception and gay marriage although he has not called for any changes to Catholic doctrine on these hot-button issues.