Martin Scorsese’s adaptation of “Silence,” Shusaku Endo’s tale of Catholic missionaries suffering brutal repression in 17th-century Japan, has met with mixed reviews. Some have found it ponderously overlong and, for those unfamiliar with Japanese history, baffling in context. It is, in fact, not a minute too long — agony and anguish can’t be rushed — and well worth the 25-year wait. Scorsese spent decades trying to realize this “passion project,” overcoming numerous production difficulties and legal wrangles along the way.

“Silence,” the 1966 novel by Shusaku Endo (1923-96), has also had a difficult life. When it was first published, Christians in Japan were urged not to read it. Today it is read across the world as Endo’s masterpiece — by Christians, too — and the variety of interpretations is striking. A further indication that the world has changed significantly in the last 50 years is that Scorsese’s “Silence” has invited so little controversy from Christian commentators.

“Silence” tells the harrowing story of Jesuit missionaries and their so-called kakure kirishitan (hidden Christian) converts set in an era when Japan began to tightly restrict European influence.

They suffer terrible persecution at the hands of a shogunate determined to rid the land of a creed it perceives as seditious: the thin end of the wedge of European imperialism.

In the climactic scenes of the film — spoiler alert — the young Jesuit protagonist, Father Rodrigues, played by Andrew Garfield, is incarcerated and psychologically worked upon both by a Japanese inquisitor and Rodrigues’ former mentor, Ferreira, who argues that Japan is a “swamp” in which Christianity will never take root. Rodrigues finally apostatizes by stamping on a Christian image — a practice known as “ebumi” (picture trampling) — in order to bring to an end the cruel torture being inflicted upon the former Christian converts.

Such a position might seem morally justifiable today, but back in the 1960s and ’70s — when “Silence” was first published — this plot device was met with outrage in many Christian circles both in Japan and abroad. In stark contrast, Scorsese’s film premiered in Rome in November after the director enjoyed a private audience with Pope Francis — who reportedly said that he had read Endo’s novel. The film was first screened to an audience of 300 Jesuit priests and then shown in the Vatican’s 50-seat film library.

How can a work that was once regarded by the Catholic Church as destabilizing now be embraced with such warmth?

Endo professed himself to be a lifelong Catholic and wrestled with the conflict between his faith and his Japanese heritage in his novels. As a young man during World War II, Endo found himself being looked upon with resentment for adhering to the religion of Japan’s enemies. After the war, Endo went to study in France, but found himself racially discriminated against by his fellow Christians in Europe. He became sickly with tuberculosis, was hospitalized and, after suffering a crisis of faith, journeyed to the Holy Land, intent on writing about the life of Christ.

For Endo, Christ was not a leader of men or a magician but someone who had endured painful doubt and who was physically weak. Jesus watched over those cast aside by everyone else: the pitiful, dirty and wretched.

Endo may have called himself a Catholic — clinging to the comfort of the religion of his youth — but the spiritual beliefs of his adult life moved in other directions as indicated by the religious beliefs the characters agonize over in his novels.

“Silence” treads a path toward conversion from Catholicism to Protestantism: Rodrigues starts off as a firm servant of his superiors in the Jesuit Order. His belief in the mediated nature of the Church and its iconography as the route to serving God is seemingly immovable. His mission in Japan has forced him to question not just his own faith but the tenets of Catholicism as he knew it until he establishes a direct communication with God himself. In the all-important apostasy scene, Rodrigues having long wrestled with doubt about why God remains silent in the face of such terrible suffering, finally hears the voice of God, clearly telling him to trample on His image.

When Endo died in 1996, two of his books were placed in his coffin: “Silence” and the 1993 novel “Deep River.” In the latter, Endo sends his protagonists to the banks of the Ganges to explore Buddhism and Hinduism in search of a kind of pantheism.

In 1965, the Second Vatican Council closed with calls for increased dialogue with other religions, but Endo’s nonconformist pantheistic ideas were, in practice, still anathema to the Catholic Church in the ’60s. The church was still fighting a fierce turf war with Protestantism and only just learning how to get on speaking terms with other religions. These days, following the advance of the ecumenical movement, there is rapprochement between the leaders of numerous world religions, whose followers huddle together in the large tent called “faith.”

“Silence” is one of the most accomplished books of the 20th century not for its straightforward representation of Endo’s ideas but for its ambiguity, which opens the text up to radically different interpretations. One of the most fascinating aspects of the novel’s reception has been the sharp division in interpretation among Christians.

In Europe, where much of the populace regards themselves as atheist or agnostic, “Silence” has often been read as a quintessential existentialist text. If there is no God, then there is no surprise that the Jesuit discovers nothing but silence on the part of the nonexistent being when terror stalks the Earth. As for the “voice of God” speaking to Rodrigues, the humanist would explain this as an “auditory hallucination” prompted by the extreme stress of persecution.

Endo himself despaired that too often the interpretation of “Silence” — as depicted in Masahiro Shinoda’s 1971 film adaptation, with its eerily dissonant soundtrack hinting at a cold, disinterested cosmos — was that, in a godless universe, the “silence of God” was a mere inevitability.

And yet in Christian America, “Silence” is still passionately discussed in theology classes, with the potential for radically different interpretations. Here the key question is not the existence of God, but “Was it God that Rodrigues heard telling him to apostatize?” For those who passionately believe that apostasy is evil, then the only conclusion could be that Rodrigues was hearing the voice of the Devil.

What is lasting about “Silence” is that far from demanding acceptance of Endo’s personal vision of Christianity, the novel is ultimately silent about finding any definitive interpretation.

The film, in all its sumptuous, haunting beauty, is faithful to Endo’s message of Christ and his concept of belief. Yet in all its accomplishment, it also reveals the power of the original novel, and of all great literature, which, as French philosopher Albert Camus wrote, “offers everything and confirms nothing.”

A new edition of “Silence,” with a foreword by Martin Scorsese, has been published by Peter Owen. Damian Flanagan wrote the introduction to Shusaku Endo’s “Scandal,” also published by Peter Owen.

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