The nuns of the Monastery of San Joaquin and Santa Ana in Valladolid were reluctant to lend Pedro de Mena’s Mater Dolorosa to the National Gallery’s new exhibition of Spanish seventeenth-century religious art, “The Sacred Made Real”. When the loan request arrived, the sixteen nuns gathered to vote on it, as they do on all important questions affecting the sorority. The rosewood ballot box was passed round and into it were placed, one by one, sixteen black marbles.

It was only when the museum sent a special emissary to plead the museum’s case that this most emphatic of refusals was reconsidered and, after much soul-searching, reversed. It was eventually decided that the Valladolid Virgin of Sorrows, a masterpiece of polychrome statuary, would be allowed to travel after all – but only on the strict understanding that the utmost respect be afforded to her. Photographs might be taken of the Virgin, but only in wide shot. There were to be no close-ups, no unfeeling paparazzi intrusions on her grief, no tactless zoomings-in on the single glass tear that trickles frozenly forever down her lightly flushed cheek.

The episode is a reminder that to many people in Spain, even today, the sculptures and paintings that have been gathered together for this boldly unusual and utterly compelling exhibition are not merely works of art. They are cult objects, holy things, touched by the numinousness of the divine. This is particularly true of the many painted statues which have been included in the show, and which collectively amount to its greatest revelation. Often life-size, they form a crowd of suffering, dying Christs, weeping Virgins and saints entranced by mystic visions.

Rarely exhibited outside Spain, these startlingly vivid figures were sculpted by generations of long underrated master-carvers and painted, with breathtaking skill, by polychromers whose names remain in many cases unknown. At the National Gallery, each is displayed in spotlit isolation, surrounded by pools of Caravaggiesque darkness. It is an apt touch, given the huge influence of Caravaggio’s later, most deeply tenebristic work on Spanish sacred art. As a result, the already gloomy basement galleries of the Sainsbury Wing have been transformed into haunted chambers of sepulchral darkness.

In this museological equivalent of “the dark night of the soul” – a phrase invented by the Spanish mystic, St John of the Cross – every space is haunted by vivid ghosts. Saint Francis Borgia, thin as a rake, contemplates his own mortality, an expression of fervent piety etched on his leathery, sunburned face. The prominent vein at his temple seems almost to twitch as he opens his heart to the joyful prospect of long-awaited death. He once held a skull and cross and although time and loss have deprived him of those accessories he still seems to see them before him.

Opposite stands St Ignatius Loyola, founder of the Jesuits, equally emaciated and clad in an abstract shimmer of black drapery. He too stares into space with deep concentration, eyes fixed on adistant sacred beyond. Loyola it was who had reaffirmed the ancient medieval Christian traditions and methods of interior visualisation, encouraging worshippers to close their eyes to the visible world and find the image of Christ within, in the world of the imagination. The image is not a memorial to Loyola but a role model inspired by his example. Look inside as he does, the sculpture insinuates, and you too may be granted a vision of Jesus Christ the saviour.

Both these images were carved by Juan Martinez Montanes, one of several unacknowledged masters revealed by the exhibition. But they were painted into startling life by Francisco Pacheco, so they cannot be described as the creation of a single individual. Polychromers and woodcarvers were paid on equal terms in seventeenth-century Spain, which itself suggests the deeply ambiguous nature of the objects produced by their collaboration. Some might say that the National Gallery should not be showing such things because it is a museum devoted to painting, not sculpture. But these wooden figures are both sculptures and paintings, at one and the same time. They slip between categories.

Montanes also carved the nearby effigy of Saint Bruno, staring fixedly at the crucifix he holds in his right hand. The paper-thin, overlapping folds of his linen-crisp white robes are a miracle of craftsmanship, so much so that it is hard to believe that this is indeed wood not fabric. The shadows in the drapery have been subtly accentuated by the polychromer, whose job it was to intensify the already uncanny realism of this life-size figure. The artist responsible may, on this occasion, have been none other than Francisco de Zurbaran, leading religious painter of the Spanish Baroque. If so, it was Zurbaran too who painted the figure’s eyelashes, stubble and solemn, living eyes.

The seventeenth century is often referred to as “the Golden Age” of Spanish art. But it was also an age of peculiarly bloody piety, as the Catholic Church sought out an art capable of rallying its worshippers against the threat of the Protestant Reformation. Among the most powerful images in “The Sacred Made Real” are a group of polychrome sculptures of Christ tortured, dying or dead. Pedro de Mena’s Christ as the Man of Sorrows, of 1673, is a half-length sculpture of Christ after his flagellation, polychromed by an unknown artist with truly disconcerting delicacy. The figure’s smooth and pallid skin is deeply mottled, criss-crossed with subcutaneous whip-bruising and flecked with blood where the flails of his tormentors have torn into the blood vessels beneath. Thin rivulets of viscous red paint trickle down Christ’s face and body from the crown of thorns that pierces his hair and forehead.

Even more gruseome, and yet more cannily manipulative of the viewer’s emotions, is the Dead Christ fashioned by Gregorio Fernandez and a similarly unknown polychromer some forty years earlier. The pale, thin, vulnerable body of the crucified Christ has been laid out on a burial shroud of carved and painted limewood, like a corpse in a morgue. The illusion of deep nail-holes in hands and feet, and of bloodied scabs at the knee caused by the long procession to Calvary, has been created by the expedient of working crusty segments of cork bark into the carved wooden body. Thick and bloody swatches of paint have been worked into the grain of the bark. The staring eyes of the dead figure are made of glass, the teeth of ivory, the deliberately chipped and broken nails formed from curls of ingeniously carved bull’s horn. Rarely can the mortification of the flesh have been evoked with such tender and meticulous care.

Such works of devotional art were meant to be – and indeed are – disconcertingly like actual human beings of flesh and blood. Ruskin derided them as the mannequins of a maddened faith and was perhaps a little scared by them too. Over the centuries, such works have roused not only devotion but also distrust. Long ago, the churches and monasteries of England were filled with medieval images very much like them: sad gilded madonnas with painted faces, carved from oak and ash by artists from Kent to Wessex and beyond. Thomas More, travelling with a group of pilgrims, was disconcerted to hear two among the company debate whether “Our Lady of Walsingham” was more or less holy than “Our Lady of Barking”. The correct answer, he snapped at them, was neither. Both images were mere “stocks” or effigies – evocations of a higher reality, but with nothing of the powers of that higher reality intrinsically invested in them. Qualms like those aroused in More would lead, ultimately, to the Reformation’s proscription of all such imagery in Protestant churches – a crushing reassertion of the Second Commandment, according to which “Thou shalt not make unto thee any graven image”.

Carved and painted Christian sculpture has a very particular, double-edged, dangerous appeal. It has always existed on the borderline between image and idol. Partly for that reason art historians, especially in the Protestant north, have been reluctant to take polychrome statuary seriously as art, preferring to dismiss it as the lumber-room kitsch of extreme superstition. That is why “The Sacred Made Real” is such a salutary and important exhibition. Not only does it allow the masters of coloured Spanish statuary into the precincts of a museum, it sets them side by side with acknowledged masterpieces of religious painting by such artists as Ribalta, Velazquez and, above all, Zurbaran. Not only do the sculptures survive such comparisons extremely well, they also emerge as crucial drivers of the entire Spanish religious aesthetic. It is very clear from this show that the compositional habits, sense of palette and tendency towards an extreme, ascetic realism of a painter such as Zurbaran cannot be understood without the influence of polychrome statuary. “The Sacred Made Real” is that rare thing – an exhibition that does not merely re-evaluate, but fundamentally realigns, the history of its chosen subject.