Poor Goya. In his lifetime he had to put up with deafness, the Spanish Inquisition and the Duke of Wellington. Now he has Jake and Dinos Chapman to contend with. The brothers called one of their earliest tributes to the great Spanish painter, printmaker and visionary Great Deeds Against the Dead - quoting Goya - in which they reproduced one of his horrific images of cruelty as a lifesize tableau featuring a dismembered mannequin impaled on a tree. Their latest work is another great deed against the dead - a desecration of the memory of Goya.

Two years ago, the Chapmans bought a complete set of what has become the most revered series of prints in existence, Goya's Disasters of War. It is a first-rate, mint condition set of 80 etchings printed from the artist's plates. In terms of print connoisseurship, in terms of art history, in any terms, this is a treasure - and they have vandalised it.

"We had it sitting around for a couple of years, every so often taking it out and having a look at it," says Dinos, until they were quite sure what they wanted to do. "We always had the intention of rectifying it, to take that nice word from The Shining, when the butler's trying to encourage Jack Nicholson to kill his family - to rectify the situation," interrupts Jake.

"So we've gone very systematically through the entire 80 etchings," continues Dinos, "and changed all the visible victims' heads to clowns' heads and puppies' heads."

The "new" work is called Insult to Injury. The exhibition in which it will be shown for the first time, at Modern Art Oxford, is called The Rape of Creativity.

Goya's Disasters of War is a precocious modern masterpiece, a work left by its creator as his final savage bequest to the 19th, 20th and 21st centuries - it was far too anti-clerical and unpatriotic to be published in his lifetime, and the first ever edition came out in 1863, three and a half decades after his death in 1828. From the very start of its public existence, it has been experienced not as a historic but as a contemporary work, its images so urgent and truthful that they function as living, new art.

And it is this colossus whose masterpiece the Chapman brothers have chosen to defile.

"He's the artist who represents that kind of expressionistic struggle of the Enlightenment with the ancién regime," says Jake, "so it's kind of nice to kick its underbelly. Because he has a predilection for violence under the aegis of a moral framework. There's so much pleasure in his work. To produce the law, one has to transgress it. Not to be too glib in the current conditions, but there's something quite interesting in the fact that the war of the Peninsula saw Napoleonic forces bringing rationality and enlightenment to a region that was presumed Catholic and marked by superstition and irrationality. And here's Goya, who's very cut free from the Church, who embodies this autonomous enlightened being, embodied as a gelatinous dead mass without redemption - then you hear George Bush and Tony Blair talking about democracy as though it has some kind of natural harmony with nature, as though it's not an ideology."

Whoah, step back a minute. Defacing a work of art is, perhaps, the last taboo of the liberal, Britart-loving, Tate Modern-going public. The crime novelist Patricia Cornwell's purchase and destruction of works by the British artist Walter Sickert in pursuit of her theory that the disturbing early-20th century painter of music hall audiences and seedy interiors was Jack the Ripper nauseated many, me included. To destroy a work of art is a genuinely nasty, insane, deviant thing to do.

The Chapmans have recently found it remarkably difficult to offend people. While their early works - the lifesize girl mannequins with penises for noses - were routinely dismissed as emblematically egregious grotesqueries of 90s British art, in the past few years they have received massive acclaim, in language they profess to find baffling and hilarious. They made Hell, a tableau in which thousands of toy second world war German soldiers mutilate and kill each other and themselves in a psychotic Nazi orgy, and had it interpreted as a profound comment on the Holocaust and its representations: "The idea of making 5,000 little toy soldiers all running round mutilating each other, and then find pathos in that - it's alarming that people are prepared to cathartically reappropriate these things which are so redundant and void," says Jake. "It took us three years to make 5,000 people. It took the Germans three hours to kill 15,000 Russian prisoners of war."

Then last autumn, they unveiled Works from the Chapman Family Collection, displayed at the White Cube gallery in sombre, museum-like conditions with the works picked out in spots of light amid the darkness; you wandered among astonishingly powerful examples of tribal art: huge carved wooden masks with raffia hair and fetish nails; then realised these were parodies, carved by the Chapmans, with McDonald's logos, scary clown faces, or features composed of burger buns.

It was, I thought, genuinely on the edge of racism and fascism - "primitive" art has been consumed by western modernism for more than 100 years, and here was an exhibition that seemed deliberately to associate African tribal artefacts with darkness and evil. And this spectacle was reviewed and hailed as a devastating moral critique of fast food, America and so on. "The 'best' reviews were the ones that pointed up this incredibly dumb and vulgar binary opposition between McDonald's bad and ecology good, as though the work was some sort of attack on globalisation," says Jake. In fact, they claim: "We want to make McDonald's into a religion."

So one reason for altering 80 original Goya prints is that it may finally offend the people the Chapmans see as their target - an audience in which they include themselves; the liberal, humanist, gallery-going chattering classes. (When asked whom he sees as the enemy, Jake says "Dinos".) It worked on me, when I first heard about it. After all, Goya's Disasters of War is not some dry old relic no one cares about - it is a work that has never lost its power to shock.

In 1863, the very year the Academy of San Fernando in Madrid published the first edition of Los Desastres de la Guerra, French modern artists watched appalled as the cynical regime of Napoleon III installed and then betrayed a puppet government in Mexico; the great modern painter Edouard Manet's painting of the end of this squalid imperial episode, The Execution of Maximilian (1867-8), emulates Goya's cynical delineation of war atrocities in its icy, close-up depiction of a firing squad killing at embarrassingly close range.

Because Goya was the first artist to reveal the gross face of war stripped of all chivalry, romance and idealism, because he captured something quintessential about modern war, all succeeding generations of artists have seen war through his eyes: they have recognised in the Disasters of War a template for their own nightmares.

During the Spanish civil war, Picasso turned back to Goya's etchings - and his paintings in the Prado, the Second and Third of May 1808 - as he planned his own anti-war masterpiece, Guernica. If Guernica mimics Goya's twin history paintings of the popular Madrid uprising against the French on May 2 1808 and its bloody suppression, his etched cartoon strip, The Dream and Lie of Franco (1937), uses the same form as the Disasters to denounce fascism. Perhaps, though, it is Salvador Dali in his paintings Soft Construction with Boiled Beans: Premonition of Civil War (1936) and Autumn Cannibalism (1936) who captures the madness and total ambivalence of Goya's etchings - because Goya, like Dali, had no faith in the forces of progress.

What we see in Goya's prints is the death throes of an idealist. Goya started as the artist of the Enlightenment, in so far as there was an Enlightenment in Spain. Brilliantly colourful and relishing the empiricism he learned from the British modern portraiture of Gainsborough and Reynolds, Goya's early paintings subtly endorse liberal-minded politicians and secular values; when Napoleon, the self-styled champion of Enlightened values, who was so progressive that he took archaeologists with him to invade Egypt, occupied the Iberian peninsula in 1807 and manoeuvred his brother Joseph on to the Spanish throne, middle-class intellectuals might have been expected to side with this alien moderniser. Instead, the popular rising commemorated by Goya's Second of May 1808 began a savage, chaotic struggle in which - it is clear from his Disasters of War - Goya found it hard to take sides: his images depict peasants torturing and desecrating the corpses of French soldiers; French barbarities against the Spanish; and the irrationality of the neoconservative return to Catholic order that followed the Duke of Wellington's driving Napoleon out of Spain (Goya's great portrait of the Iron Duke is in London's National Gallery).

It is the disabused nature of Goya's Disasters of War that makes them so compelling; other artists saw the Napoleonic wars in romantic and, indeed, Romantic terms - Antoine-Jean Gros's astonishing picture, Napoleon Visiting the Plague Victims at Jaffa, in the Louvre, gives the emperor Christ-like powers and clearly makes him a quasi-religious figure; the British claimed that he in fact ordered the slaughter of 3,000 Turkish prisoners when he captured Jaffa.

Goya's modernity has never exhausted itself; he was as immediate to Picasso and Dali as he was to Manet; of all pre-modern artists, he is the one who most resembles a modernist. This is who the Chapmans have victimised.

But, of course, it's not quite as it seems.

Apart from Goya's surviving proofs - above all, a unique album with his handwritten captions in the British Museum's prints and drawings collection - there are no entirely "original" sets of the Disasters; published posthumously, it does not even have Goya's original title - he called the etchings "Fatal consequences of the Bloody War in Spain against Buonaparte and other Emphatic Caprichos".

The Chapmans' series is from a - historically very significant - edition published directly from Goya's plates in 1937, as a protest against fascist atrocities in the Spanish civil war; its frontispiece is a photograph of bomb damage to the Goya Foundation. Given how important the Disasters of War were to Picasso, Dali and the image of the civil war, this is clearly an important, evocative, emotionally raw thing, and they have scribbled all over it.

Yet the antecedent they themselves claim puts the gesture in a different light. In the 1950s, points out Jake, the American artist Robert Rauschenberg erased a drawing by Willem de Kooning, the great abstract expressionist painter. On the face of it, Rauschenberg was being aggressive - as a younger artist, a founder of pop and conceptual art, he was erasing the work of the older, dominant generation in a flamboyantly oedipal gesture. Yet he said he chose De Kooning for this fate specifically because he admired him; and he sought the older artist's permission. Destruction can be an act of love.

And whatever you think of the Chapmans, you can't deny the systematic and consistent nature of their interest in Goya. They have been reworking him since the early 90s; as well as their lifesize Great Deeds Against the Dead, there was a miniature tableau of all the atrocities in the etchings, and then, at the same time as they were working on Hell, they produced their own series of etchings inspired by Goya's Disasters - combining motifs from Goya with Nazis, volcanos and cartoon horror.

For some critics, this is all a callow waste of energy. It seems pathetic to take the most powerful of all artist-moralists, an artist who needs no apology or explanation and for whom the deadening phrase "old master" seems utterly inappropriate, and make these sterile simulacra, these crass copies. The critic Robert Hughes, who is writing a book on Goya, has dismissed the Chapmans' translations of his images as superficial exercises.

But we live in ahistoric, depthless times, not least in art, and it's getting hard to be unimpressed by the sheer dedication of the Chapmans. The artists themselves claim they prefer to be despised as banal anti-humanists than praised piously as humanists. The language of praise we use for art is amazingly limited; if we like a work of art, we feel compelled to find depth, anger, moral fervour, spiritual truth - all the things the Chapmans claim to reject.

The new works are not in the studio when we talk about them. I feel I have a pretty good idea of the Chapmans' approach to Goya, so I don't worry too much about this. We talk about criticism and the way it resorts, always, to the humanist rhetoric of moral, emotional and political meaning. We laugh at the pious things the art critic of the Sunday Times said about them.

It's all very sophisticated. The next day I see the images. I think they are brilliant and profound. Oh dear. Somehow, they do not destroy, but find something new in the Disasters of War. The Chapmans use the word "evil" to describe the atmosphere that pervaded their recent ethnographic show; there is a wild sense of evil in what they've done to Goya. The altered prints make you think a serial killer with an addiction to drawing psychotic clown faces has got into the British Museum's prints and drawings room - like the killer in Red Dragon who eats an original Blake.

Violet and white bursts of colour, the clown heads and puppy faces are astonishingly horrible. They are given life, personality, by some very acute drawing, and so it's not a collision but a collaboration, an assimilation, as they really do seem to belong in the pictures - one art historical antecedent is Max Ernst's collages in which 19th-century lithographs are reorganised into a convincing dream world. What the Chapmans have released is something nasty, psychotic and value-free; not so much a travesty of Goya as an extension of his despair. What they share with him is the most primitive and archaic and Catholic pessimism of his art - the sense not just of irrationality but something more tangible and diabolic.

The Chapmans have remade Goya's masterpiece for a century which has rediscovered evil. And I have fallen into their trap.

· Jake and Dinos Chapman: The Rape of Creativity, April 12 to June 8, Modern Art Oxford, 01865 722733.