In a statement, the Vatican said the newly issued report by the UN Committee on the Rights of the Child would be "submitted to a thorough study and examination," saying it remained committed to protecting children.
"The Holy See does, however, regret to see in some points of the Concluding Observations an attempt to interfere with Catholic Church teaching on the dignity of human person and in the exercise of religious freedom," the statement noted.
In the report released Wednesday, the UN watchdog demanded that the Vatican "immediately remove" all clergy who are known or suspected child abusers and heavily criticised the Vatican's stance on homosexuality, contraception and abortion.
The watchdog denounced the Holy See for adopting policies allowing paedophile priests to sexually abuse children and said it was gravely concerned the Vatican had not acknowledged the extent of the crimes committed.
The report and lambasted the practice of transferring paedophile priests from parish to parish within countries and sometimes abroad.
This practice places "children in many countries at high risk of sexual abuse, as dozens of child sexual offenders are reported to be still in contact with children," the report said.
The Holy See should open its files on members of the clergy who "concealed their crimes" so that they can be held accountable, it concluded.
It also called on a commission created by Pope Francis in December to investigate all cases of child sexual abuse "as well as the conduct of the Catholic hierarchy in dealing with them".
Last month, UN experts grilled a Vatican delegation in Geneva on why the Holy See had refused a UN request for data on paedophile priests and what it was doing to prevent future abuse.
While denying an official cover-up, the Vatican said it only released such information if requested to do so by another country as part of legal proceedings.
The Vatican in July 2010 introduced more stringent disciplinary guidelines in the wake of the sex abuse scandal. Involving hundreds of cases sometimes dating back many decades where minors were molested by priests and other clergy at Church-run institutions and parishes across several continents, the scandal undermined the Catholic Church's moral authority.