When David Yallop enters a bar or a restaurant he scans the room for anybody whose presence might make him uneasy. Call it paranoia, but he always chooses a seat with its back to the wall. Such caution is understandable in a man who entered Beirut with a price on his head. On that occasion he was on the trail of the international terrorist, Carlos the Jackal, and now, not for the first time, the might of mitres is about to be swivelled in his direction with the publication of his latest investigative opus.

It has taken Yallop more than eight years to write The Power and the Glory, the goal of which is to de-sanctify a man on the road to sainthood: the late Pope John Paul II. Yallop, who describes himself as a Catholic agnostic, is aware that many will regard this work as heretical. Others will see it as the inevitable sequel to his previous book, In God's Name, which exposed the web of financial corruption within the Vatican and explored the suspicion of murder surrounding the death of John Paul I, "the smiling Pope", whose reign lasted 33 days.

But for most of the 27 years of John Paul II's pontificate this was a Pope acclaimed as one of the most charismatic leaders of our time. Even so, he was a paradoxical figure, an autocrat who was loved; the Pope of crowds, whose intractable orthodoxy nevertheless caused many of the multitude to fall away. So, two years after the death of this pilgrim the question increasingly asked is whether his papacy was a failure.

"His obituaries abound with myths, fantasies and dis-information" says Yallop. "The cult of personality which John Paul so revelled in focuses precisely on the man but at great cost to the faith." Even that vision of the Pope as a sad and frail figure, suffering from Parkinson's disease, fails to temper Yallop's criticism. He remembers being told by an informant in those final weeks that "the actor within the Holy Father is dying hard. He refuses to walk off the stage. He is a man terminally drugged on the adulation of the audience."

Yallop begins his demolition work on the heroic reputation of the man, born Karol Wojtyla, by knocking down the perception that in Poland he confronted the Communist regime. "The myth of John Paul, conqueror of Communism, is just that," he says. Yallop accuses the late Pope of complicity "with some of the worst dictators". He claims that John Paul's opposition to liberation theology along with his condemnation of contraception, divorce, abortion and homosexuality caused a haemorrhaging of followers by marching the Church back to the dark ages.

But the most explosive chapters inevitably concern the author's ongoing research into "the Vatican's financial scams" and its systematic cover-up of child sex abuse cases. Of the first he writes: "Because of his (John Paul's) continuing failure to make the necessary decisions', a corrupt archbishop (the American, Paul Marcinkus) retained control of the Vatican Bank for a further decade."

Of the second transgression, Yallop maintains that the Pope's inability once again to make the "necessary decisions" meant that clerical sexual abuse continued unchecked, resulting in mass desertions from the faith. "The late Pope and his cardinals had known since the early 1980s that such abuse was widespread but instead of taking early and decisive action, their response was secrecy."

Yallop is recognised as one of the world's most substantial and unflinching investigative writers. Now 70, he looks back on a life punctuated with dangerous assignments which have included tracking down the Colombian drug cartels and delving into the identities and mind-set of the bombers of Pan Am Flight 103. The sales of In God's Name exceed six million, and it was awarded the Crime Writers' Gold Dagger Award for the best non-fiction book of 1984.

Even he can not deny the impact of the Pope's first visit home to Poland after his election in 1979. Descending from the plane, the man who had almost become an actor before be became a priest, knelt and kissed the ground. In Warsaw's Victory Square he addressed a million of the long-suffering faithful.

No Communist country had experienced anything like it, and from that moment the world would watch this handsome, hitherto unknown, inheritor of Peter's rock who, at 38, had become a bishop, a cardinal at 47 and pontiff at 58. This was the spectacular outsider who had broken the 455-year-old Vatican tradition of choosing an Italian Pope. Yet to Yallop's eye, such scenes were down to superlative theatrics. "Yes, he was a very political Pope, but I believe there was no real compassion in his papacy."

In his view, Karol Wojtyla was elected by the College of Cardinals to put a brake on the progressive theology initiated by Pope John XXIII at the Second Vatican Council of 1962. That spirit of reform would have continued under the papacy of John Paul I, Albino Luciani, the gentle liberator. The cause of his death was officially given as myocardial infarction but Yallop believes it was murder, a heart attack induced by poisoning.

On May 13, 1981 John Paul II was struck by bullets from a potential assassin's gun as he toured St Peter's Square. Mehmet Ali Agca, already wanted for a slaying in Turkey, his native country, was sentenced to life imprisonment in an Italian jail.

In Wojtyla, the Neo-cons of the Vatican had opted for a Pope of the nineteenth century. "That is the key to his personality. His father was born in the same decade that papal infallibility was created, and that teaching would have been very fresh in the minds of the Wojtyla family as Karol was growing up. I mean, intellectually the Pope was back in the 1870s and 1880s: no partnership with his fellow bishops. No collegiality. No dialogue or discussion, merely an unquestioned primacy that inevitably atrophied."

Yallop returns to the subject of corruption within the Vatican Bank which was under the chairmanship of Chicago's Archbishop Marcinkus. Known as a bit of a bruiser from his days playing American football, and from acting as a papal bodyguard, Marcinkus rose to become "gatekeeper" of the Vatican Bank without ever acquiring the necessary ability or integrity for such promotion.

By 1968 the Vatican decided on a major switch in banking policy, away from Italian assets in favour of US and offshore investments. It was a decision that led to a series of criminal and financially disastrous relationships that threatened its entire moral reputation. To maximise profits, Marcinkus had formed an unholy alliance with Michele Sindona, frontman for the Mafia, Lucio Gelli, master of Italy's powerful and illegal P2 Masonic Lodge, and Roberto Calvi, the banker whose body was found under Blackfriars Bridge in London in 1982, and who had been the Mafia's money- launderer and paymaster to P2.

Charges of tax evasion, racketeering and fraud raged, but Marcinkus avoided being placed in the Italian witness box by using his diplomatic immunity, and always insisted that he had never knowingly done anything wrong. Yallop believes his disgrace would have happened much sooner had John Paul I lived longer. "He intended to remove Marcinkus, and if he had, the crash that occurred only after Calvi died would have taken place in 1978." Calvi and his conspirators had been robbing his Banco Ambrosiano for years. "And when he was suicided', as I put it, the authorities found a hole in the bank's finances of $1.3bn."

But if John Paul II's predecessor was poisoned because the removal of Marcinkus would have exposed the scandal, who was the murderer? "After investigating a list of suspects, I have no doubt that it was Gelli's P2 lodge which he ran as a state within a state and whose power was extraordinary."

But the most shocking content in Yallop's book refocuses attention on that gravest of crimes, the repeated violation of innocents. Why did John Paul II close his eyes for so long to paedophilia among errant priests, the sin which, more than any other, has riven the Church worldwide? The Church's attempts to bury these appalling breaches of trust have only compounded the suspicion that parishioners had placed their trust in an institution more concerned with protecting its worldly goods against litigation than with healing the wounds inflicted on children by sexual deviants.

Yallop says that it wasn't a case of the Pope being kept in the dark. "Well into his papacy he went on tour to Austria where priests had been trying to remove Cardinal Hans Hermann Groer, a practising paedophile, for years. But Wojtyla would hear nothing bad about the man, and he chastised those priests who had gone semi-public about their concern."

HANS Groer resigned "on grounds of old age" in 1995 but by then thousands of Austrian Catholics had defected to create their own sect. For many this episode confirms that John Paul was not always a good judge of character. "He was fundamentally weak. Now, that will surprise you because what comes across is a man of great strength . . . But, in fact, the way he handled the Second World War indicates something else. Contrary to the stories that were published when he became Pope, he was not among those who had risked their lives trying to save Jews and Poles from the Nazis. Wojtyla elected for quietism."

Yallop asserts that if it hadn't been for the Communists he would never have become Pope. The regime had approval on the selection of bishops, and when the diocese of Krakov became available, it was made clear that the regime would reject all nominations except Wojtyla.

"The Communists knew he wasn't going to rock the boat. I don't know if that was an overt corruption of the soul but it was certainly a latent one. It was only when he became Pope that Wojtyla condemned anti-Semitism."

As a "Catholic agnostic" Yallop rarely goes to Mass but he does pray. "There are good priests out there, and in the Vatican, too. Of course there are. And to those Catholics who feel that what I've written is a betrayal I would say that since In God's Name was published 23 years ago I've received thousands of supportive letters, and only seven which were really critical of me."

Yallop still has half a dozen books he wants to write, and investigating will involve risk. "I've had attempts on my life but I don't talk about them because that might encourage more." Yet, he recalls that when he was abroad publicising In God's Name, a newspaper rang his wife to ask if she was worried about the Mafia coming to kill him. "She replied that she didn't think the Mafia would be able to find Crouch End. Quite charming, really."

However, even the most faithful have been surprised by Pope Benedict's decision to fast-track John Paul II towards beatification and sainthood. Could it be that the Vatican wishes to canonise the late Pope before further books like Yallop's destroy the aura? "That's a very astute observation. After all, why rush things? The point about beatification is that it's a long and measured process. "

As for the future of Catholicism, Yallop sardonically reflects that the succession of Cardinal Ratzinger as Pope has proved that there is life after death: "With Benedict at the helm, the reign of Wojtyla continues." And, talking of afterlife, does the residual Catholic in Yallop worry that he might be storing up some trouble for himself?

"Well, I'm not sure about an afterlife," he says, then amends that reflection by musing that if there is something going on up there, he has every confidence they'll know he is on their side. The Power and the Glory: Inside the Dark Heart of John Paul II's Vatican , by David Yallop, is published by Constable, priced £20.