It is often said that art galleries today are the new cathedrals – places that people visit to replenish the spirit in a secular age. But for many centuries, cathedrals functioned in the manner of art galleries. Walk into any cathedral in Western Europe, and you will discover countless examples of beautiful art works, from intricate wooden carvings and metalwork to moving marble sculptures and exquisite painted altarpieces.

“After Classical antiquity, Christianity became the predominant power shaping European culture,” explains Jennifer Sliwka, curator of art and religion at the National Gallery in London. “After Theodosius I made Christianity the official state church of the Roman Empire in 380, works commissioned for any spiritual, civic or political purpose were meant to reflect this new belief system.” As a result, Sliwka points out, “Roughly one third of the paintings in the National Gallery’s collection of Western European art are of religious subjects – and nearly all of these are Christian.”

In galleries of modern art, however, the proportion of works treating Christian subjects is much smaller. After centuries of artists actively soliciting the patronage of the church, religion and art are no longer such natural bedfellows. Indeed, in the wake of modernism, it sometimes feels as though art and religion are now strangers to one another, or even downright hostile. “When visiting a contemporary gallery or art fair, I rarely expect to see works that treat religious subjects,” says Sliwka.

Shock doctrines

When contemporary artists tackle Christian subjects today, they often do so in an iconoclastic, ironic, disrespectful or subversive fashion. Think of the Italian artist Maurizio Cattelan’s satirical sculpture La Nona Ora (1999), in which Pope John Paul II lies on a red carpet, crushed by a meteorite that has just plummeted from the heavens; or Piss Christ (1987), a photograph by the American artist Andres Serrano, in which a small plastic crucifix is submerged in a glass of urine.

When Chris Ofili’s painting The Holy Virgin Mary (1996) was exhibited in New York in 1999, the city’s then-mayor, Rudolph Giuliani, took exception to the artist’s vision of a black Madonna with a bare breast moulded from elephant dung: “The idea of having so-called works of art in which people are throwing elephant dung at a picture of the Virgin Mary is sick,” Giuliani said.

Yet contemporary artists who wish to make less critical art about Christianity are not the endangered species you might think. And in some cases the church is even reprising its role as an important patron of the arts. Last week, for instance, St Paul’s Cathedral in London unveiled Martyrs, a new video installation by the American artist Bill Viola.

It isn’t the first time that St Paul’s has embraced contemporary art: in 1983, the cathedral commissioned the sculptor Henry Moore, whose travertine-marble Mother and Child now sits in the north quire aisle. But Martyrs is the first permanent moving-image artwork ever to be installed in a British cathedral or church. “This is a big moment in the history of religious art,” the art critic Martin Gayford wrote in The Daily Telegraph. “This is the first time that moving images will take a prominent place in one of the great cathedrals of Christendom.”

Positioned behind the cathedral’s High Altar in the south quire aisle, Martyrs is a multi-screen “video altarpiece” in which four different individuals are subjected to life-threatening trials, as the elements of earth, wind, fire and water rage around them. One man remains seated as a conflagration threatens to consume him. Another is hoisted aloft on an upside-down crucifix before a torrent of water overwhelms him. A shackled woman twists and turns, buffeted by a tornado, while a fourth person arises from a mound of earth.

“It is a compassionate work,” says Mark Oakley, the Canon Chancellor of St Paul’s who oversaw the Viola project since its inception 11 years ago. “Those people are alone with their faith and their conscience, and they are dying for something that they believe is worth dying for. And inevitably that question is thrown back onto us: we’re really faced with ourselves here. There is a dignity and a beauty and a peace about what’s happening to them too – something is being transformed. I believe that Martyrs is enigmatic but very profound. The rumour of God is alive in it.”

In good faith

Viola is not the only contemporary artist in recent years who has contributed to the time-honoured tradition of religious art without resorting to satire or mockery. The British artist Mark Wallinger, for example, has made several artworks that draw upon the machinery of religion and explore questions of faith. These include Ecce Homo (1999), a life-size, white-resin cast of a young man representing Christ that was placed temporarily on top of the Fourth Plinth in Trafalgar Square.

“There are several contemporary artists working today that treat religious subjects more directly without undermining them,” says Sliwka. “Ana Maria Pacheco, for instance, often chooses religious subjects such as the beheading of the Baptist to refer back to a familiar Biblical story but also to use it as a political example of one who speaks ‘truth to power’ and to draw attention to the troubled political history of her native Brazil, referring back to violence generated by colonialism and African slavery.”

Moreover, last year, the Holy See exhibited at the Venice Biennale for the first time – though, as Sliwka points out, “The works chosen for their pavilion deliberately steered clear of work that engaged directly with Catholic themes or imagery.” She continues: “Often contemporary works that explore spiritual themes more broadly – like the video installations of Bill Viola – are more successful with audiences today who tend to represent a variety of beliefs, backgrounds and lifestyles.”

Perhaps surprisingly, then, given that we live in an era that is becoming ever more secular, the great tradition of Christian art appears to be alive and well. “Cathedrals in particular have worked quite hard in recent years to encourage contemporary artists to bring their work into the cathedral,” says Oakley. “We’re all looking for a resonant, universal language with which we can explore questions that you might call spiritual. And for many, the religious vocabulary is no more, it isn’t resonant, so we need to find shared forms that we can utilise to start the conversation – and art is one of them. The heartland of religion is about the laboratory of the spirit: it’s about spiritual growth and development and transformations. So I’m not at all surprised that when artists engage with people of faith, they find that there’s a lot of overlap in terms of shared interests and concerns. Contemporary artists have an enormous amount to offer to the church – and vice versa.”

Alastair Sooke is art critic of The Daily Telegraph.

If you would like to comment on this story or anything else you have seen on BBC Culture, head over to our Facebook page or message us on Twitter.