Yesterday Pope John Paul issued an unprecedented public apology for past wrongs committed in the Catholic Church's name. At a special ceremony in St Peter's Square he asked forgiveness for sins of intolerance and violence against dissidents, wars of religion, and the Inquisition. He also begged pardon for excommunications, persecutions and sins against the Jews; the church's failure to speak out against injustice; sins against peace and the rights of peoples; and sins against women.

John Paul pressed ahead with the initiative in the teeth of opposition from many cardinals; and his apology to the Jews, especially, echoes numerous condemnations of anti-Semitism he has made over the past two decades. Few doubt his sincerity. Unlike Pius XII, the wartime pope whose ambivalent attitude towards the Third Reich has drawn charges of cowardice and upset plans to declare him a saint, John Paul suffered at first hand in a Nazi labour camp.

Why then has his statement prompted sharp criticism, as well as admiration? Many Catholics - let alone those outside the church - naturally feel that the apology has been issued scandalously late. But it also comes hard on the heels of a Vatican declaration that Pius IX, a notoriously anti-Semitic 19th century pontiff, is to be beatified on September 3. The move will place him in line to be declared a saint soon afterwards; but as Professor Owen Chadwick, Britain's foremost church historian, comments: "Pius IX's [record] verges on the criminal."

Pius IX (born Giovanni Maria Mastai-Ferretti), a symbol of unbending resistance to the modern world, reigned for a record period between 1846 and 1878. He is chiefly remembered for proclamations on the immaculate conception (1854) and infallibility (1870), and for his condemnation in The Syllabus of Errors of anyone who held that "the Roman Pontiff can and should reconcile himself with progress, liberalism and modern civilisation".

His anti-Semitism, though not untypical of the period, caused dismay even to many contemporary Catholics. As the world has now been reminded, in 1858 the papal police in Bologna entered the home of a Jewish couple and abducted their six-year-old son. Their pretext was that the boy, Edgardo Mortara, had been baptised, while dangerously ill, by a housemaid several years earlier. Edgardo was detained and subsequently adopted by Pope Pius, who refused to give him back to his distraught parents unless they converted to Catholicism.

Even when seen in the most sympathetic light (Pius clearly believed he was saving Edgardo from damnation), this record is hardly synonymous with sainthood. Why should the present Pope - an intellectual who says he welcomes dialogue between theology and other disciplines, and a staunch advocate of human rights - now be giving his blessing to a figure as ignominious as Mastai-Ferretti?

The decision is a mark of the deep contrasts and contradictions in John Paul's character. Though a lifelong critic of the right and leftwing dictatorships he lived under before his election, this Pope has been happy to accept or extend an authoritarian style of church government. His approach to saint-making - avid, controversial and unchallengeable - is as clear a mark of his conservative agenda as the Vatican's regular silencing of independently minded theologians has been.

Normally, a prime requirement of beatification is that a cult should have arisen around the candidate in question. Though an icon of resistance to the Risorgimento during his lifetime, Pius has signally failed to satisfy this test. He will be beatified on the same day as Pope John XXIII, a figure of genuine stature who opened the Catholic church to the modern world through the Second Vatican Council of 1962-65.

The joint ceremony will form a coded warning that liberalism can only operate within strict limits, and take place soon before an equally contentious service to beatify several hundred "martyrs" from the Spanish civil war.

"The irony of infallibility," says Owen Chadwick, "is that it places limitations on popes because they can't contradict their predecessors." (The doctrine was first invoked during the Renaissance by Franciscans who told the then pope that he could not contradict an earlier pontiff's declaration that Christ had lived in poverty.) A Catholic historian who wishes not to be named goes further. "Not being able to condemn a predecessor is one thing. But affirming a former pope so explicitly is quite another. John Paul II's action is a disgraceful abuse of his authority."

• Rupert Shortt was formerly assistant editor of the Tablet

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