With a hawk-like face and a mind as sharp, Rupert Thomson alights at a table in the British Library cafe.

He curls himself around a mug of tea as if hiding schoolwork from the boy at the next desk but, although the subject of his artfully spare, compelling new book is subterfuge, deceit and concealment, on the subject of himself the 57-year-old novelist is engagingly open and frank.

Secrecy is a powerfully dark, bittersweet story about a real-life sculptor of miraculously lifelike wax figures. Set at a time when the Medicis controlled Italy's most sinister city, it was, Thomson admits, an odd choice of subject: "I knew nothing about the 17th century. I knew nothing about Florence. I knew nothing about wax."

Despite a degree in medieval history and political thought from Cambridge, he realised so much research was necessary before he could write a word that he waited years before tackling it. In the meantime, he published two novels, including the acclaimed Death Of A Murderer, about a policeman who guards Myra Hindley's corpse on the night of her death, and, even more controversially, his memoir This Party Has Got To Stop. A breathtakingly honest work, it describes the volatile aftermath of his father's death, an event which resurrected the trauma he and his younger brothers suffered after the death of their mother nearly 20 years earlier, when he was only eight.

As all 10 of Thomson's books attest, his imagination is vivid, even wild, and while there is sometimes a dreaminess about his prose, in person he has a sparkling wit and a theatrical talent for telling a good story. It soon becomes clear that the tale behind the writing of Secrecy is worthy of a novel itself. The book began, he explains, when a friend dropped by for dinner. At the time, Rupert and his girlfriend Kate were caretaking a 300-year-old farmhouse near Montepulciano in Tuscany.

"I know exactly when it happened," he says in a clear, south-coast English accent that hints at his Eastbourne childhood. "It was January 16, 2000, because my girlfriend was pregnant. Recklessly we'd gone there to have the baby, when she was six months pregnant. God knows why we did that. It seems not just cavalier in retrospect, but idiotic. It was our first child, it was an IVF child, so it had been difficult to become pregnant, and there we were in the middle of nowhere. My girlfriend didn't speak Italian, and the house was underwired so you could only have one electrical appliance on at once. If you turned on the washing machine, you had to turn off the only radiator in the house."

Over dinner, their guest told Thomson about La Specola, a zoological museum in the heart of Florence, which had exhibits of wax figures she knew he would like. Intrigued, he paid it a visit.

"I walked into a room and there were these three hip-high glass cases containing naked women," he says. "The women had their heads on satin pillows, real human hair, glass eyes. They were naked and yet walked this fine line between medical and erotic. You couldn't tell what they were for."

In that instant, the germ of the idea was planted for Secrecy, in which Sicilian sculptor Zummo is commissioned by Cosimo III, Grand Duke of Tuscany, to create (in strict confidence) a life-size naked woman. This he does, using the corpse of a drowned girl, whom he begins to suspect has been murdered. As this daunting artistic project unfolds, Zummo finds himself drawn into a net of lies surrounding the Grand Duke, which threatens not only his own life but that of his spirited lover, Faustina.

When I comment on how beautifully Secrecy is written, Thomson beams: "I've always wanted to write something that was beautiful and I think I might have done it this time. My brother called it romantic – and I suppose it is. Obviously it's not Mills & Boon, but it's got that quality about it."

A Russian doll of a novel, in which one story leads to another, its composition partly reflects the manner in which Thomson writes. Secrecy, he estimates, had gone through 12 drafts to reach its finished state. This process would exhaust most writers, and with this particular book it certainly created a new sensation for its author: "When I was doing the proofs, I had this feeling that the book was some kind of lost classic that I hadn't written at all, that it had always been there. It was a really peculiar feeling. It was as if it was nothing to do with me. It was as if I had unearthed it, and brought it to light."

Asked why he thinks this was, he hesitates. "Well, someone once said of one of my novels, it has future classic written all over it. I'd like to think it will be something that will last. I'm just feeling it sooner than I should." He laughs, but soon adds: "I don't mean to sound arrogant. It mystifies me."

There's more than a little mystery in Thomson's life. When his daughter Evie was born, problems escalated. After he collected Kate and the baby from hospital for the long drive home, it began to snow, and he started to feel very unwell.

"I had heard there was this epidemic of flu sweeping the country at the time, and people had died – a footballer in Rome. By the time we got back to the house, I knew that's what I had. I remember telling my girlfriend in the car, 'I think I'm coming down with this flu,' and she said, 'You can't, I need you.' I got back to the house, rang the hospital and described my symptoms and they said, 'Get the baby out of the house. It could be really dangerous.'"

A neighbour took them in and Thomson went to bed. "It was this extraordinary fever - I remember taking off my T-shirt and it was so wet it slapped on to the floor. And in the middle of all this I could hear a voice calling my name, from outside, and I'd drag myself over to the window, and open the window, and it was Kate standing in the snow saying, 'You've got to get better. I can't do this on my own.'"

Kate believed it was psychosomatic, he says, "to make the point to her that I was not to be counted on to take responsibility for this child".

How did he respond to this? "Well, it's a theory. It's possible. Because, as an eight-year-old boy, I did have to take responsibility for my two younger brothers when my mother died suddenly, I had to become a kind of mother to them, or a father. My father was disabled, so he was weak. So I remember this sense of taking on a big responsibility when I was too young for it. It's possible I felt in some part of me that I had had children and didn't want to go through it again. As a theory it kind of stands up. But, also, I was really ill. It could have just been a really untimely illness."

After this, it is perhaps not surprising that the idea of children, and fatherhood, play a pivotal role in Secrecy. But so do women. When I ask about the significance of having a perfect but silent wax woman at the centre of the story, Thomson looks serious.

"The trouble is, with a question like that, I start thinking about my mother, and then it all gets cod-psychological, and I don't really want to. It's the idea there is in my life this unknown, beautiful woman who I can't remember. There's a paragraph early on in the memoir where I say that - I can sort of remember the dresses she used to wear, but I can't remember her inside them. There's this absence that perhaps I'm always trying to fill. It revolves around women rather than men for obvious reasons."

But there is another absence in his life which, while small, is revealing. When I ask why his brother's surname, which is on the jacket of the novel, is Farquhar-Thomson, he explains: "I was born Rupert Farquhar-Thomson. You can imagine what they used to call me at school – that Scottish name that looks so beautiful written down, and is so exotic some people have said, 'Are you part Arabic?' – but it also translates into some choice swear words, as you can imagine.

"I dropped it when I was 20, 21, when I first decided to be a writer. Then I changed it by deed poll a bit later. I didn't like it because it made me sound privileged and grand, and I wasn't, so it gave a false impression. To have the name Rupert is bad enough. I often think I should have changed everything aged 20. Rather like Eric Blair – George Orwell – because I don't think the name Rupert has done me any favours."

Descended from a Borders family of Johnstones, he says: "I think I'm only about one-eighth Scottish, but it's a nice little nugget of Scottishness."

"Originally," he adds, "the Thomson was on its own, but my grandfather, I think it was, or my great-grandfather, created the double-barrelled name, because his father had run off with the governess -"

But perhaps it's best to stop there. Otherwise, as with all Thomson's gripping tales, this story could run and run.

Rupert Thomson is at the Aye Write! Festival, Mitchell Library, Glasgow, on April 13, at noon. Tickets cost £8 from 0141 353 8000 or www.ayewrite.com.