The documentary by "Panorama" was aired late on Sunday evening and based its case on what it described as a secret document written in 1962 that sets out a procedure for dealing with child sex abuse within the Catholic Church.
Under the guidelines of the document, the "Crimen Sollicitationis", the child victim, the priest dealing with the allegation and any witness must swear an oath of secrecy - the result of breaking the oath being excommunication, claimed Panorama.
"The procedure was intended to protect a priest's reputation until the church had investigated, but in practice it can offer a blueprint for cover-up," the BBC documentary said.
"The man in charge of enforcing it for 20 years was Cardinal Joseph Ratzinger, the man made Pope last year," reporter Colm O'Gorman said in the programme "Sex Crimes and the Vatican".
Cardinal Cormac Murphy-O'Connor, head of the Catholic Church in England and Wales, has responded to the documentary with plans to write to Mark Thompson, director general of the BBC, which defended its documentary.
"The protection of children is clearly an issue of the strongest public interest," it said in a statement, responding to the bishops' criticism. "The BBC stands by tonight's 'Panorama' programme, and invites viewers to make up their own minds once they've seen it."
Responding to the documentary, Archbishop of Birmingham, the Most Rev Vincent Nichols, said the BBC should be "ashamed of the standard of the journalism used to create this unwarranted attack on Pope Benedict XVI".
He said there were two strands to the documentary, one highlighting cases of child abuse by priests -- a crime the Catholic Church dealt with seriously, carefully and with transparency -- the other attacking the Vatican.
"This aspect of the programme is false and entirely misleading," Nichols said in a statement endorsed by the bishops of England and Wales.
"It is false because it misrepresents two Vatican documents and uses them quite misleadingly in order to connect the horrors of child abuse to the person of the Pope." The second document cited by the BBC was a 2001 update of the original text.
Archbishop Nichols, chairman of the Catholic Office for the Protection of Children and Vulnerable Adults (COPCA), said the broadcaster should be ashamed by the standard of its journalism.
He said: "Viewers will recognise only too well the sensational tactics and misleading editing of the programme, which uses old footage and undated interviews. They will know that aspects of the programme amount to a deeply prejudiced attack on a revered world religious leader. It will further undermine public confidence in Panorama."
He added, however, that the programme was a reminder of the need to work ceaselessly in the protection of children.
The Pope was previously head of the Congregation for the Doctrine of the Faith, the Vatican department that enforces doctrine, from 1981 when he was still Cardinal Ratzinger, until his election as Pope in April, 2005.
The Vatican said Monday it was studying the document in question but offered no further comment.