It is uncanny that Hisham Matar's second novel should be published in this month of all months: the news seems intent on writing it a last chapter. Matar, whose first book, In the Country of Men, was shortlisted for the 2006 Booker prize, spent his early childhood in Tripoli. His father, Jaballah Matar, was a leading dissident against Muammar Gaddafi's dictatorship. In March 1990, after the Matar family had moved to Cairo, Jaballah Matar was abducted by Egyptian secret service agents, and subsequently imprisoned in Libya's notorious Abu Salim jail. At the time Hisham was 20; in the two decades since, he has lived with the tortured uncertainty of his father's fate  Jaballah Matar was last sighted alive in 2002. This book, like all of Matar's writing, it seems, has been created in the psychological shadow of that fact.

In a brief and despairing plea for closure to his father's story, written in the Guardian last year, Matar concluded with this sentence, describing his limbo: "Where is the man whose pipe stands in a cup with the five pencils I sharpen every morning? His coat hangs in my wardrobe. Maybe it still fits him?" Anatomy of a Disappearance seems to have been written with those pencils, and to take account of what it might be like to fill that jacket. It has a dreamlike quality, in spite of Matar's cool and lapidary prose. It is a fable of loss, and an often troubling meditation on fathers and sons. It is dedicated, of course, to JHM.

To begin with, though, this seems to be a tale about mothers. The book is told in the voice of Nuri, who was a young boy of eight, we discover, when his mother died. His loneliness has taken on the shape of the Cairo apartment which he shares with his father and their servant Naima. It subsequently finds its complicated object in a young woman called Mona, a fantasy in an outrageously yellow swimsuit, whom Nuri meets beside a pool while holidaying with his father in Alexandria. Mona instantly becomes both a mother substitute and an adolescent sexual torment: "the yellow strap running across her back brought to mind the yellow hospital bracelet that had been bound round my mother's wrist". When his father falls for her too, this torment is complete. Nuri is 13, Mona is 24, his father 37. Crucially, in this triangle, Nuri feels himself not only closer in age to his obsession but he also claims proprietary rights: "I saw her first." He collects glimpses of Mona, contrives intimacies, weaves a narrative that makes subsequent realities even harder to substantiate.

By the laws of this myth, Nuri's father and Mona marry. Nuri is sent away to boarding school in Yorkshire, in part, he believes, as an acknowledgement of competitive lust for his father's new wife. Matar is deft at evoking the bloodless emotional landscape of "Daleswick" and its contrasts with the pulse of life in Cairo. Nuri receives what he hopes are symbolic gifts from his stepmother by mail: exotic pyjamas, a directive to read Wuthering Heights. The scene shifts and Nuri and Mona find themselves in Montreux, at the beginning of the Christmas vacation, waiting for his father's arrival; they get word instead that he has been abducted by agents of the Egyptian state, in the dead of night, and from another woman's bed. What follows is a carefully paced unravelling of the few certainties that Nuri had thought he could rely on, and a precise confessional about the cruelty and vulnerability of adolescent desire. Nuri wanted to be his father, "his elegant, tailored clothes, his perfectly manicured fingers, and that defiance in his eyes". Now that he has acquired some of that role, a power over Mona, perhaps a complicated place beside her in bed, he quickly understands that he should have been careful what he wished for.

The book builds quietly, always concentrating on the particulars of time and place, in Geneva, Paris, London and Cairo in the 1970s, to dramatise not only the conflicts of coming of age but also the strategies by which we might respond to loss. When Nuri observes, "There are times when my father's absence is as heavy as a child sitting on my chest", or that "There has not been a day since his sudden and mysterious vanishing that I have not been searching for him, looking in the most unlikely places. Everything and everyone, existence itself, has become an evocation, a possibility for resemblance", we are aware that Hisham Matar is writing from the heart.

Given his own biography, you might expect the novel's mystery to have the solace of a conclusion, closure, even a happy ending. Matar is too scrupulous to contemplate that; the book was completed in November last year, when uncertainty, no doubt, still seemed an absolute. It is to be hoped, it goes without saying, that in the coming weeks, reality will finally be more generous to him than he has allowed his fiction to be.

Hisham Matar has one overwhelming subject, the lost father. His new novel begins with it: "There are times when my father's absence is as heavy as a child sitting on my chest." That heavy subject has a powerful autobiographical compulsion. Matar, of Libyan parentage, is a citizen of the world: brought up in New York, Tripoli and Cairo, he lives in London. His father, a rich businessman and an anti-Gaddafi activist, "disappeared" in 1990 from Cairo and was taken to a Libyan prison; it is not known whether he is alive or dead.

In the Country of Men, Matar's first novel, shortlisted for the Man Booker in 2006 and more compelling and moving than ever when read today, is told by a nine-year-old Libyan boy, Suleiman, who shows us the terrible events in Tripoli in 1979 as he sees them  kidnappings, surveillance by the military police, show trials, public executions on the television of "traitors" working against the Revolutionary Committee, the crushing of student protests, families fleeing into exile in Egypt. The family is split by the nation's cruel politics: the mother thinks the anti-government activists are "foolish dreamers", the father is working for "a better Libya". The cry goes up, then as now: "How long, how long must we bow our heads?"

The boy is obsessed with the mysterious absences and reappearances of his businessman-activist father, who is arrested and tortured, and betrays his fellow conspirators. The son, too, lets his best friend down (a bit like the boy in the bestselling 2003 Afghan novel The Kite Runner, by Khaled Hosseini). As he grows up, he will recognise in himself "a shameful pleasure in submitting to authority". The novel shows by implication how a political system of repression can warp an individual's character. Suleiman's parents send him away to Cairo; he never sees his father again, and is reunited with his mother only 15 years later. He leads a diminished life; absence and loss seep into every corner of this beautiful, short book like a miasma. But it's not only the absence of loved ones: the boy is taught the history of Libya's ancient past, and is taken to see the ruins of the Roman town of Leptis Magna. "Absence was everywhere"; "the only things that mattered were in the past".

Suleiman is intensely close to his mother, an alcoholic and thwarted feminist, married off to his father at 14. In Anatomy of a Disappearance, again the narrator is an only child with a sad mother, but this time she is silent and melancholy, not angry and explosive, and she dies when the boy is 10. Nuri el-Alfi is 14 when the novel starts in 1972. His family has been living in Egypt since 1958, when they fled to Paris, and then to Cairo, from "our country". That country is unnamed (why?), but is evidently Iraq. The mother's favourite writer is a famous Iraqi poet, Badr Shakir al-Sayyab. The father, the wealthy son of Arab silk-merchants, was a diplomatic adviser to the "young king", shot in the head in the palace courtyard in the revolution  just as Faisal II was killed in the revolution of 1958. Nuri's father continues to work, as an "ex-minister and leading dissident", towards a time "when the country comes back to us". His son thinks of it as a "secret obsession". He reads nothing but histories of his country, looking for his name in the index. His life of plotting is also a life of daydreaming. "It was all so long ago." The father's hidden activities, urgent and dangerous in the first novel, here seem obscured and mysterious, more dream-like, less close up.

What is close up is the adolescent son's painfully confused emotions about his potent, stylish father, his dead mother and his father's sexy, alluring second wife, with whom Nuri falls adoringly in love the moment he meets her. Mona's appearance in a dazzling yellow swimsuit at a hotel swimming pool in Alexandria makes a dramatic overture to a complicated triangle. Her reckless leading on of the boy; his jealousy of his father, who packs him off to a Yorkshire boarding school; his longing in exile; the accidental intimacy Nuri and Mona are thrown into when the father disappears; their eventual estrangement  all this makes up the novel's central, awkward, unhappy story. Under it, more quietly, there is another  in the end, more important  relationship, with the servant Naima, brought from Cairo to work in the household at 13, and closer to Nuri than he imagines. Her life's service to the wealthy family is a fine study of dependency, and the boy's careless treatment of her is poignantly done.

Anatomy of a Disappearance is spare and pared down. The quest for the missing father through clues and contacts, in London, Geneva and Cairo, has the feel of one of Brian Moore's later books  The Statement, or Lies of Silence  where character and depth are streamlined into taut, fast thriller mode. I missed the vivid sense of a particular city at a particular moment that In the Country of Men had, and I didn't find the teenage Nuri quite as involving a narrator as the nine-year-old Suleiman. But what is powerful, again, is Matar's sombre gift for absence and longing. As Nuri returns after many years to his father's flat in Cairo, to be looked after again by the family servants, sleep in his father's bed, work in his study, wear his watch, try on his clothes and wait for his return, we understand that it is not only the father who has disappeared, but the son too, a life lost inside loss.

Hermione Lee's Biography: A Very Short Introduction is published by OUP.