ARRIVING to interview Michel Faber, I feel both awestruck and slightly puzzled. His new novel, The Book of Strange New Things, has given me more spiritual inspiration than anything I have read for years, and features the most persuasive and likeable Christian missionary I have ever encountered in fiction. Yet Faber is reportedly an atheist.

Great novelists can do empathy, of course: perhaps this idiosyncratic Highland-based author is inhabiting the mind of faith in the same way as he took on the life of a Victorian prostitute in his best-selling novel The Crimson Petal and the White. But I cannot help thinking that there is more to this than meticulous research: I wonder whether this is a man who knows Christian spirituality from the inside.

As if to compound that suspicion, the figure who greets me in the lobby of Canongate Books, in Edinburgh, bears a passing resemblance to some desert mystic. Faber is dressed entirely in black, with a mop of blond hair that renders him younger than his 54 years, and he is barefoot after a rain-soaked walk.

He listens with priest-like curiosity as I confess that his book induced in me a kind of homesickness for a faith that I now often struggle to muster. Does he identify at all with that faith - or that struggle?

"I would say that I'm fully and thoroughly atheist," he says, gently, after a pause. "But, unlike many atheists - and certainly unlike atheists of the Richard Dawkins kind - I don't see that as any credit to me. I don't regard it as having been clever enough to leave childish things behind and evolve to the next phase of humanity, where we don't need religion any more."

His eyes grow watery. "I'm very sad that I lost my faith, and I'm very sad that it's not there to sustain me in the sorrows that I've had to deal with in my life, particularly the loss of my wife."

IT HAS been less than four months since Eva, his partner of 26 years and long-term literary collaborator, died of multiple myeloma, an incurable cancer that was first diagnosed in 2008.

A former nurse, Faber was her carer in her last years, sleeping beside her on a camp bed in hospital in the final months. That he is able to proceed with his book tour so close to her death strikes me as remarkable - and, it emerges, a testament to the uncanny ways in which the novel reflects and honours their close relationship.

"I'd already written several chapters of it when Eva got diagnosed; so I certainly didn't conceive of it as a book whose purpose would partly be to let me grapple with the impending loss of her." He speaks carefully, as if verbally traversing a room strewn with broken glass. "But, yes, it ended up doing that."

The novel opens with a man and his wife who face an unthinkable separation. Peter has been selected to be a missionary to the indigenous people of a far-flung planet named Oasis; but, to do so, he must leave his beloved Beatrice behind on earth.

Both of them are robust but compassionate Christians, and the couple's increasingly anguished correspondence punctuates the story as Peter's attempts to minister to the Oasians distance him from the dystopian nightmare unfolding for Bea back on earth.

It is a strange and compelling tale, freighted with big themes of faith, hope, suffering, and human frailty. Peter earns early respect at the human space colony for delivering a genuinely moving funeral oration, then wrestles painstakingly with the "strong liquor" of the King James Version in order to render scriptures accessible to the other-worldly Oasians.

Later, in one of the book's most moving - and eerily prophetic - moments, he ministers at the death-bed of one of the alien converts, unable to bring healing.

"One of the terrible ironies that hangs over this book is that Eva had one of the few remaining cancers that's incurable," Faber says, whose character encounters that perennial stumbling block of Christianity: on what criteria does God cure or not cure? "It's clearly nothing to do with the intrinsic goodness of a person, or their potential to make the world a better place. That would have been one of the questions that led to my losing my faith at the age of 12."

BROUGHT up in the Baptist tradition in Melbourne by Dutch immigrant parents, the young Faber was running the church library when the narrative of his belief first began to unravel. Familiar with many of the Evangelical texts of the 1970s (indeed, he named his protagonist after the best-selling evangelist Peter Marshall), he remembers his doubts multiplying as he stuffed envelopes with missionary magazines bound for Papua New Guinea.

"When you read something that has been dumbed down in order to be comprehensible by a very foreign culture, it puts the whole Evangelical exercise into quite an unflattering light," he says. "It seems so disrespectful of nuances, of people's intelligence, or of the specifics of their own experience."

He broke the decision of his unbelief in a note left on the kitchen table. Deeply disappointed, his father reacted by forcing him to tell the church himself. "My mother was just sorrowful that she wouldn't meet me in heaven. And it was pretty much left alone after that - we didn't discuss it."

He began to write in earnest soon after this time, continuing through university in Melbourne and the "militant atheism" of his twenties, working in casual cleaning jobs, and later nursing. But it was only after his emigration to Scotland, in 1993, and with the crucial encouragement of Eva, that he entered, and won, his first short-story competitions, and was approached by his publishers, Canongate. The eerie and genre-defying Under the Skin was his first critical success in 2000 (and was adapted as a film last year, starring Scarlett Johansson).

His novels are famous for being utterly unlike one another; and it is just as difficult to see any common attitude to religion. His rewriting of the Promethean legend, The Fire Gospel, in 2008, was as much a satire on publishing as it was on religion, focusing on the manuscript of a hapless apostle which undermines the divinity of Jesus.

Meanwhile, in The Crimson Petal and the White (2002), his biggest hit to date, Faber tells me that his favourite characters were the love-struck Victorian Christians, who were later dropped by the BBC in its TV adaptation.

NOTABLY absent from his work are the pitiably flawed, hypocritical, or corrupt believers so familiar elsewhere in literary fiction. "There's a stack of books that will do that for you if you're inclined to see faith that way," he says, wearily. "And I didn't want to add to that stack."

Instead, the new novel is ultimately an exploration of human empathy, our need to find meaningful connection. And, in the context of the terrible suffering and death that sometimes ensue, Faber sees no intrinsic advantage in an entirely materialistic universe. Quite the opposite: "I really doubt that atheism will get you through," he says, bluntly.

"I suppose the trick that a humanist has to play on him- or herself is to live as if there were a God. I'm really not convinced that you can live fully while seeing yourself, and all those you love, as parcels of meat."

Shored up against his darkest moments, meanwhile, Faber chronicles tantalising synchronicities, flashes of inexplicable grace. "I certainly believe the Shakespearean cliché that there's more to heaven and earth than is dreamt of in your philosophy; and I know that there are things that happen in our lives that are completely inexplicable within a scientific framework."

Moments before our meeting, for example, he bumped into a long-lost friend in the street, only days after wishing that he had some contact details so that he could inform him of Eva's death.

It makes me wonder whether he believes in a soul - something that is not just body - that transcends us. Faber is quiet for a moment. "I'm almost at the beginning of my grieving; so I expect there will be other phases of the journey to come. But, at this point, I feel that Eva is a canister of ash, and that is all she is right now. I don't feel she's here with us.

"I feel that she lives on in a philosophical sense, in that I've been very much changed as a person by having had the privilege of being her partner for 26 years; but I think she had her life, and it's over."

He lets that settle, then adds: "But I don't know what's in store for me - I might change my mind if you interviewed me again in six months."

THIS openness feels qualitatively different from the Dawkins school of atheism. Faber cites the position of the former Bishop of Edinburgh the Rt Revd Richard Holloway, who conducted Eva's funeral. "He still goes to church, even though he has lost his faith, because he says it's easier for him to be in the presence of that absence than to close the door on it entirely."

He rubs thoughtfully at a long red scab on his forearm - a bite from his cat, sustained shortly before starting his book tour. "In the next few days, this will fall off, and my skin will be perfect again - and is that not mind-bogglingly miraculous?"

He smiles for the first time. "The more logical outcome would be what happens with fruit when you damage it. So we really are immensely privileged, in a way that I don't think we're sufficiently grateful for."

I ask if gratitude is a philosophy that he can inhabit in his darker moments. The frown returns. "Well, I'm caught perfectly in between, because I'm very grateful for the body that I still have, and the planet that I'm still allowed to enjoy; but I've just lost my wife, whose body was ruined in exactly the way that an apple gets ruined, and who isn't able to enjoy the planet any more. So there's a big question mark over that right now."

What is clear is that, even in death, Eva continues to exert a positive influence on him, just as she originally encouraged him to seek a publisher, served as his closest editor, and, in her final days, urged this habitual introvert out into the world with a book that she knew and loved in its entirety.

"Eva really cherished every day," Faber says. "She was the sort of person who wakes up in the morning and thinks: what fun can I have today in this amazing place? In the early years, when I had a lot of negative attitudes, shading into mental illness, when she got particularly frustrated with me, she would say: 'You are sinning against life.'"

Faber cannot imagine the writing process without her - indeed, he has shocked readers by stating that The Book of Strange New Things will be his last novel. Yet it is clear that Eva's particular brand of non-religious hope remains the closest thing he has to a spiritual practice.

"It is a very cruel irony that she's gone," he says, quietly. "But I feel that the least I can do to honour her is to sin against life less than I used to - to cherish it more, appreciate it more. And that's what I'm trying to do."

Nick Thorpe is the author of Urban Worrier: Adventures in the lost art of letting go (Abacus).

The Book of Strange New Things by Michel Faber is published by Canongate Books at £18.99 (Church Times Bookshop £17.10 - Use code CT265 ).