At low tide, Shigetsugu Kawakami can just about make out the “forbidden” rock from his home overlooking the beach in Neshiko, a tiny village on Hirado island in southern Japan.

According to verbal testimony, at least 70 villagers were taken there and beheaded in the early 17th century. Their crime had been to convert to Christianity. “When we were children, the adults told us that if we climbed on to the rock the village would be cursed,” said Kawakami.

Today, “ascension rock” is a permanent reminder of the atrocities of almost four centuries ago. But the martyrdom of Japan’s “hidden” Christians is in danger of being forgotten.

Tens of thousands of Japanese Christians were executed, tortured and persecuted after the Tokugawa shogunate banned the religion in the early 1600s. With a wary eye on Spanish rule in the Philippines, the authorities feared Japan could be the next country targeted by European powers that used Christian teachings as a catalyst for colonial rule.

The ban left Japan’s 750,000 converts with a choice: renounce their religion or continue to practise their faith in secret, in the knowledge that discovery would almost certainly mean death.

Discussion of Japan’s Christian heritage has largely been absent from public life since the mid-1960s, when Shusaku Endo explored the martyrdom of early converts in his critically acclaimed novel Silence.

Now, Martin Scorsese hopes to ensure their story will not be forgotten with a film based on Endo’s novel that is due for release next year.

Starring Liam Neeson and Andrew Garfield, the film – also called Silence – follows two Portuguese Jesuit missionaries who are sent to Japan in the early 1600s to investigate reports that their mentor has committed apostasy. They arrive to find Japanese converts in the midst of a brutal crackdown by the Tokugawa shogunate.

While no official records are kept of the number of modern-day kakure kirishitan (hidden Christians), local experts say perhaps only a few dozen people still consider themselves believers.

Once its saviour, clandestine worship has contributed to a sharp decline in the number of believers. Combined with dwindling, ageing populations on the islands where it once flourished, believers fear their crypto-Christian tradition is at risk of dying out.

Kawakami, 64, is one of the few hidden Christians who is happy to talk publicly about his faith. “We don’t practise our faith in public because we are effectively still in hiding,” he said. “We usually remain quiet and never ‘out’ ourselves as Christians by appearing on TV or giving interviews. We don’t hold special ceremonies or pray in public. In fact, we don’t do anything that would risk giving ourselves away.”

Remote southern islands such as Hirado proved fertile ground for Catholicism after St Francis Xavier and other missionaries introduced it to Japan in 1549. After a nationwide ban was enforced in the early 1600s, converts devised ingenious ways to keep their faith alive.

They gathered in private homes to conduct religious ceremonies, and figurines of the Virgin Mary were altered to resemble the Buddha or Japanese dolls. To the uneducated ear, their prayers sounded like Buddhist sutras, even though they contained a mixture of Latin, Portuguese and obscure Japanese dialects. Scripture was passed on orally, since keeping bibles was considered too great a risk. None wore crosses or other religious accoutrements.

The need for secrecy during the 250 years that Christianity was banned meant the version of the religion observed by Kawakami’s ancestors bore little resemblance to its mainstream Catholic origins. Instead, early Japanese Christians incorporated elements of Buddhism and Shinto into their faith until it became a polytheistic creed of its own.

“In many ways it was a very Japanese version of Christianity,” said Shigeo Nakazono, curator of the Shima no Yakata museum on Ikitsuki, an island near Hirado.

But even this localised form of Christianity met with fierce opposition from the Shogunate authorities, who devised a singularly cruel test of loyalty to expose converts. Suspects were ordered to prove they were not Christians by trampling on fumie – images of Christ or the Virgin Mary carved from stone or wood – or face being hanged upside down over a pit and slowly bled to death.

When the Meiji government lifted the ban in 1873, an estimated 30,000 secret Christians came out of hiding. Now, Christians of all denominations make up less than 1% of Japan’s population of 128 million.

“Japan was coming under the influence of European industry and technology, and that meant that old objections to Christianity weakened,” Nakazono said.

Nakazono wondered whether Scorsese’s film would stay true to Endo’s novel, which some have criticised for being preoccupied with martyrdom. “If all hidden Christians had been martyrs, there would have been none left,” he said. “But there were enough people willing to stamp on the fumie, denounce Christianity and then beg God for forgiveness.”

At Neshiko beach, ascension rock – physical proof that there were those who refused to abandon their faith – is half submerged by the incoming tide. Even today, centuries after the last execution, locals remove their shoes before setting foot on the beach’s fine white sand as a sign of respect.

Like the rituals of the kakure kirishitan, the memories of the executed converts have been preserved by word of mouth – a tradition that gives Kawakami hope that their courage, and beliefs, will not be forgotten.

“We feel we have a duty to pass it on to future generations,” he said. “This is something our ancestors risked their lives to tell us.”