Rupert Thomson, in an interview, compared the creation of a novel to the art of the sculptor  the patient coaxing of beauty, meaning, definition, out of something as solid and shapeless as a lump of wood or marble. Perhaps it is unsurprising, then, that he was drawn to flesh out a sculptor of his own, the Sicilian narrator of Secrecy, his ninth novel. Gaetano Zummo worked in wax at the end of the 17th century; his works can still be seen in the La Specola museum in Florence, but the artist himself remains an enigma. Scant details are known about his life  just enough to offer a tantalising prospect to a novelist with an eye for ambiguity.

A new novel from Thomson is always keenly awaited by his fans, not least because he never fails to surprise readers from book to book; the form and setting of his novels are as diverse as the characters who inhabit those worlds. He has satirised the advertising industry in Soft, conjured a dystopian, segregated Britain in Divided Kingdom, plunged into pornography and the aftermath of abuse in The Book of Revelation and obliquely considered the life of Myra Hindley in the Costa-shortlisted Death of a Murderer. Through all his fiction, so wildly different on the surface, runs a unifying thread of the macabre, a haunting, dream-like dissociation from reality.

Secrecy is, on the surface, a more straightforwardly historical novel, peopled with a number of real characters. In common with the best historical novelists  writers such as Hilary Mantel, Rose Tremain, Andrew Miller or Iain Pears  Thomson takes the facts and makes of them a framework over which he layers a rich emotional life that feels at once entirely true to the period and yet wholly recognisable.

Zummo is driven as an artist by the desire to endow his creations with this elusive quality of ambiguity; what the English collector he meets at the Medici court calls "liminality". Throughout his narrative, he scatters fragments of his own past, so that the reader gradually comes to understand the secret that has shaped his destiny and left him a fugitive, unable to return to his home town. "Secrecy could be imposed from without, like a punishment or an affliction," he says, "but it could also be cultivated, or even willed. It could offer comfort."

Zummo is best known for the macabre tableaux that reveal his fascination with corruption and death: small theatres where lifelike figures lie contorted, dying of plague while bodies decompose around them. These works catch the attention of the grand duke of Tuscany, Cosimo III, who invites him to Florence and offers to become his patron.

Far from being a haven, Florence seduces him into greater danger. An air of menace infects the city, and especially the Medici court, where Zummo makes an enemy of sinister Dominican Padre Stufa. Strict laws governing sexual propriety are enforced. Jews are banished to a ghetto. People are arrested and tortured on hearsay. It is a city of shadows, watchful eyes, whispering tongues, where the mistrust and paranoia that Zummo's itinerant life has bred in him seem to find their natural fulfilment. The grand duke mourns the absence of the wife who never loved him, and reveals to Zummo his secret commission: he wants the sculptor to make him a lifesize figure of a beautiful young woman.

Zummo must cast her from life, but despairs of finding any corpse flawless enough, until one day his physician friend tips him off in secret that a young woman has been found naked and murdered on the riverbank. It is only when Zummo begins to make the moulds of her body that he discovers the image of a dog's head carved into the skin of her neck: the signature of her killer. The danger of the secret commission takes on even greater urgency as Zummo comes to realise that a trap is closing around him.

In this liminal world, where every character guards his or her secrets, most dangerous of all are the secrets protected and nurtured by women: the dead girl and her wax counterpart; Faustina, the young Florentine woman with whom Zummo falls in love, or Marguerite-Louise d'Orléans, the Duke's estranged wife, to whom Zummo is narrating this history at the end of his life. The secrets of birth are more potent, and more deadly, than the secrets of death.

Or perhaps, in the end, the two cannot be separated. The novel is structured as a series of stories-within-stories, each opening up to reveal another narrative hidden inside it, echoing one another and mirroring the secrets Zummo builds into his wax artworks.

Thomson's writing is pitch-perfect here. His prose is as clear and limpid as water, his ear finely attuned to the timbre of the period though mercifully free from archaisms, his characters drawn with subtlety and wit. The details are pin-sharp, but sparing enough not to weigh down the story. Instead, there is a mesmerising quality to the unfolding of the narratives and a sense of ellipsis that keeps it hovering on the threshold of reality and calls to mind the dreamlike flavour of Alessandro Baricco's Silk. Secrecy is beautifully plotted, too; not a scene or an exchange wasted, as the characters' secret pasts are glimpsed in fragments and eventually woven together towards a fleeting resolution.

Thomson is a writer of exceptional skill, though his work has perhaps not been celebrated as widely as it deserves. Secrecy may be the book to change that. It is surely his finest novel to date: exquisitely crafted, with the power to possess and unsettle the reader in equal measure.

One of the most extraordinary  and most hidden  spaces in a city of rare and remarkable treasures is the suite of rooms in Florence's La Specola that houses the natural history museum's collection of baroque anatomical waxes (pictured). These halls are almost always empty of visitors, which renders first sight of their exhibits even more eerie: to walk into them for the first time is like entering a macabre fairytale. In glass cases lie full-sized female figures in wax, limbs delicately positioned to replicate feminine life: they wear pearl necklaces, they have real, waist-length hair, their skin gleams  and their bodies have been laid shockingly open to demonstrate the red and yellow organs of digestion and reproduction.

Around the pale-green walls vitrines show every imaginable body part sculpted in wax, depicting gestation, anatomy and disease with shocking vividness  and yet the most startling of the wax rooms' revelations is to be found in the teatrini of Gaetano Zumbo, the Sicilian master of wax Cosimo III summoned to his court in 1691 and the subject of Rupert Thomson's masterly new novel.

Created in the baroque period that followed the great flowering of the Renaissance, Zumbo's plague pieces, housed in miniature theatres of inlaid wood, are bizarre masterpieces, precisely evoking the intersection of art and science, of magic and reason that Florence once represented. With admirers as various as Herman Melville and the Marquis de Sade, they are infinitely more alive than tableaux usually are; their tiny figures, pinkly living or green with decay, evoke mortality and illustrate the transience of human glory alongside the stages of syphilitic degeneration. They are transparently the product of an imagination both possessed and unfettered, and as such it is hard to conceive of a more appropriate pairing of novelist and subject than that found here. Something of a literary Renaissance man himself, across eight novels and a memoir Thomson has moved like Zumbo with elliptical grace and genre-defying freedom between the surreal, the historical, the interior and the concrete modern worlds: he has been compared to JG Ballard, Dickens and Buñuel.

And in Secrecy all his considerable gifts  for binding an audience tight into his narrative, for rich characterisation, for originality of vision, for delicately intuiting a lost world as well as amply researching it  are exercised in parallel.

Opening in rainswept France with the dying Zumbo's visit to Marguerite-Louise of Orleans, Cosimo III's degenerate, estranged wife, the book quickly transports us back to the sculptor's arrival in Florence 10 years earlier. The Medicis' power  spiritual, cultural and economic  is in dramatic decline and the court to which Zumbo is summoned is a savagely repressive one. Adulterers and fornicators are transported about the city in bloodstained prison carts and the decapitated heads of sodomites are mounted on the battlements of the Bargello: for Zumbo, trailing rumours of nameless perversions since his abrupt departure from Sicily, it is already a dangerous place. Far from protecting him, the artist's patronage by the Grand Duke, involving as it does both a darkly secret commission and becoming Cosimo's confidant in a jealous court rife with spies and poisoners, winds him only tighter in the net.

When Zumbo falls in love with a subversive young woman called Faustina on the dubious margins of the Grand Duke's circle and uncovers a labyrinthine treachery, all the elements of a deeply satisfying page-turner are in place  while at the same time more subtle pleasures are also in play.

As he unfolds his narrative, moving from Florence to Sicily and back again, dipping into the intrigues of the court and tracing the city's geography, building character and layering historical and psychological detail with deliciously measured slowness, Thomson transcends genre pretty effortlessly. He doesn't scrimp on the many satisfactions of a historical novel  in particular an exotic profusion of detail, from the composition of wax (beeswax, carnauba, leadwhite) to the construction of baroque fireworks, from vultures and peacocks in the Boboli gardens to the scent of violets at a Medici ball  and he provides an unstintingly gripping thriller plot into the bargain.

But what lifts Secrecy to a more rarefied level altogether is the visionary imagination that overlays the scrupulously worked structures those genres demand. It informs the brilliance of Thomson's characterisation, from the morbid monomania of a tormented Cosimo, to the brutish, coiled savagery of the Dominican enforcer Stufa, to the ghostly sadness of a neglected child. Along with a particular poetic gift for laying the exquisite alongside the visceral, it enables him to evoke Florence's peculiarly sinister magic to perfection, and to thread together the real, the historical and the purely imagined with such loving attention that I defy readers to see the join. Indeed, the join becomes irrelevant.

 Christobel Kent's novel, A Darkness Descending, will be published by Atlantic in May.