The Pope played a leading role in a systematic cover-up of child sex abuse by Roman Catholic priests, according to a shocking documentary to be screened by the BBC tonight.

In 2001, while he was a cardinal, he issued a secret Vatican edict to Catholic bishops all over the world, instructing them to put the Church's interests ahead of child safety.

The document recommended that rather than reporting sexual abuse to the relevant legal authorities, bishops should encourage the victim, witnesses and perpetrator not to talk about it. And, to keep victims quiet, it threatened that if they repeat the allegations they would be excommunicated.

The Panorama special, Sex Crimes And The Vatican, investigates the details of this little-known document for the first time. The programme also accuses the Catholic Church of knowingly harbouring paedophile clergymen. It reveals that priests accused of child abuse are generally not struck off or arrested but simply moved to another parish, often to reoffend. It gives examples of hush funds being used to silence the victims.

Before being elected as Pope Benedict XVI in April last year, the pontiff was Cardinal Thomas Ratzinger who had, for 24 years, been the head of the powerful Congregation of the Doctrine of The Faith, the department of the Roman Catholic Church charged with promoting Catholic teachings on morals and matters of faith. An arch-Conservative, he was regarded as the 'enforcer' of Pope John Paul II in cracking down on liberal challenges to traditional Catholic teachings.

Five years ago he sent out an updated version of the notorious 1962 Vatican document Crimen Sollicitationis - Latin for The Crime of Solicitation - which laid down the Vatican's strict instructions on covering up sexual scandal. It was regarded as so secret that it came with instructions that bishops had to keep it locked in a safe at all times.

Cardinal Ratzinger reinforced the strict cover-up policy by introducing a new principle: that the Vatican must have what it calls Exclusive Competence. In other words, he commanded that all child abuse allegations should be dealt with direct by Rome.

Patrick Wall, a former Vatican-approved enforcer of the Crimen Sollicitationis in America, tells the programme: "I found out I wasn't working for a holy institution, but an institution that was wholly concentrated on protecting itself."

And Father Tom Doyle, a Vatican lawyer until he was sacked for criticising the church's handling of child abuse claims, says: "What you have here is an explicit written policy to cover up cases of child sexual abuse by the clergy and to punish those who would call attention to these crimes by the churchmen.

"When abusive priests are discovered, the response has been not to investigate and prosecute but to move them from one place to another. So there's total disregard for the victims and for the fact that you are going to have a whole new crop of victims in the next place. This is happening all over the world."

The investigation could not come at a worse time for Pope Benedict, who is desperately trying to mend the Church's relations with the Muslim world after a speech in which he quoted a 14th Century Byzantine emperor who said that Islam was spread by holy war and had brought only evil to the world.

The Panorama programme is presented by Colm O'Gorman, who was raped by a priest when he was 14. He said: "What gets me is that it's the same story every time and every place. Bishops appoint priests who they know have abused children in the past to new parishes and new communities and more abuse happens."

Last night Eileen Shearer, director of the Catholic Office for the Protection of Children and Vulnerable Adults said: "The Catholic Church in England and Wales (has) established a single set of national policies and procedures for child protection work. We are making excellent progress in protecting children and preventing abuse."

Panorama: Sex Crimes And The Vatican is on BBC1 tonight at 10.15pm.