The Roman Catholic church is bracing for a new public backlash after agreeing to participate for the first time in a television documentary series about the Inquisition, its 600-year-long campaign across Europe against heresy which formally ended only 40 years ago.

The four-part American-made series, which begins tonight on the UKTV History Channel, is based at least in part on archives which the Vatican only formally opened to scholars in 1998, though church records from other parts of Europe of such events as the notorious trial of the astronomer Galileo have long been published. The revelations drawn from the church's meticulous recording of its persecutions have forced officials on to the back foot, leaving them claiming that its behaviour in the campaigns to root out error and unorthodoxy, during which many thousands of people were tortured and killed, were really not too bad, or at least only in keeping with the standards of prosecution of the time. Kings and Protestants were also enthusiastic torturers.

The series interviewed the Very Rev Joseph Augustine Di Noia, the New York-born priest now under-secretary for the Congregation of the Doctrine of the Faith, the church's successor to the Inquisition, which was formerly headed by Cardinal Joseph Ratzinger, now Pope Benedict XVI. Possibly the highest ranking Vatican offi cial ever to be interviewed publicly on the subject, Di Noia told the documentary makers: "It is a mistake to torture people. However, torture was regarded as a perfectly justified, legitimate way of producing evidence and it was therefore legally justified. Killing people over ideas, generally speaking, seems to us not to be a very good idea after 2,000 years of history . . . and generally we disapprove deeply of this kind of purgation, but it seems to me it is possible to understand it within the context of its times and also to understand it within the sociology of religion, how communities react to threats which they regard to be dire or fatal."

The attempt to put the Inquisition in context, despite several hundred years of condemnation of the church's behaviour, is recognised as probably a lost cause even by Professor Agostino Borromeo, the Italian historian, whose ancestors include nine cardinals, at least one pope and a 16th century saint, who was entrusted by the Vatican with editing a scholarly symposium on the newly released archives in 1998. Prof Borromeo says surviving documentation indicates just a small minority of heretics were executed, because only the truly unrepentant were burned at the stake. There were rules about punishments according to age and sex and limits to the length of torture. Torture and execution were always carried out by the secular authorities, not church officials.

"Torture was a method of proof, the best proof, the queen of proofs," he said. "Torture was not invented by the Inquisition, but heresy was regarded as so dangerous that it was allowed. This is not an apology for the institution, but modern studies have revised the black legend and as historians we have to record that."

Nevertheless, two years ago, Pope John Paul II issued an apology for the Inquisition. The files in the Vatican archives are far from complete and have not yet been fully investigated. Despite being studied by historians for the last eight years, only about 10% of what survived has been examined, Prof Borromeo estimates.

Monsignor Charles Burns, the Glaswegian former deputy chief of the Vatican's secretarial archives for 35 years, is not surprised. He guarded the church's diplomatic, chancery and exchequer papers stretching back more than 1,000 years - probably the greatest and oldest institutional archive in the world, which occupies more than 100km of shelf-space.

"Oh yes, there are wonderful things there," said Father Burns. "What other archive would have a letter from Ghengis Khan's nephew, the love letters of Henry VIII to Anne Boleyn and the letters of Lucretia Borgia, showing what an accomplished, Princess Diana-like young woman she must have been? It is a Pandora's box."

But unlike British government archives which are released after 30 years, the Vatican has only got up to 1922.

Prof Borromeo thinks it is too late to change the image of the Inquisition, even though he thinks the correct picture of its activities has now emerged. "You cannot project backwards our modern morality to a society which did not know toleration, in politics as well as religion. Even one death for heresy is a problem."