When Emma Brockes was 10 years old, her mother, Paula, announced: "One day I will tell you the story of my life, and you will be amazed." Fifteen years later, as Paula lay dying, the details finally began to come out. Brockes thought she already knew her mother's story. Born in South Africa in 1932, Paula lost her own mother when she was two, after which her father remarried. Having grown up with seven half-siblings in a series of remote hamlets in what was then Zululand, now Kwa-Zulu Natal, she emigrated to England in 1960. Marriage and motherhood in a rural corner of Buckinghamshire followed. "When I gave her childhood any thought at all, I thought it sounded kind of fun; like Cider with Rosie, but with deadlier wildlife." Now it seemed there was more. When Brockes's mother was in her mid 20s, she revealed, Paula had had her father arrested. "There had been a highly publicised court case, during which he had defended himself, cross-examining his own children in the witness box and destroying them one by one. Her stepmother had covered for him. He had been found not guilty." After this, Paula had deliberately cut herself off from her former life.

What exactly was it that Paula had accused her father of? Having only her mother's belated, incomplete hints at domestic violence, and possibly worse, to go by, Brockes – who is a journalist – sets out to uncover the truth. The result is this courageous, clear-sighted book, which shifts between memoir and elegy as it examines the persistence of family secrets and the fragile interface between innocence and knowledge. Why not let the past well alone? Where such secrets are concerned the choice, as Brockes argues, is often "not between knowing a thing and not knowing it, but between knowing and half knowing it, which is no choice at all".

And what a story it is. When Paula escapes South Africa, the possessions in her trunk include a six-piece dinner service and a gun, objects that point both to her desperate desire for gentility and the concealed brutality of the life she is leaving behind. Brockes describes her mother in late middle age as a debonair and knowingly mysterious figure who likes to present herself, in the tranquil village where she lives with her husband and daughter, as a "Woman of the World in a Town Full of Hicks". As Brockes begins to dig, she realises to her horror that behind what she had always regarded as a flourish of character, "an actual solid event had existed". With hindsight, some of this horror coalesces around the family photographs, of which several are reproduced here. They show Paula as a baby with her parents; her mother cheerful but frail (she would soon die of tuberculosis), her father Jimmy, wavy-haired, in shirtsleeves, holding his daughter in his arms. Later the snaps show Paula as a toddler putting flowers on her mother's grave. Jimmy worked in the Natal gold mines and as an engine driver and the family was not well-off. Following his second marriage, there are photos of Paula's half-brothers and sisters from the 1950s, the girls in print dresses, their hair carefully teased. The desired image, projected against a backdrop of veldt and dust, is always one of determined respectability.

In the library at Colindale, however, Brockes learns that before her grandparents were married, Jimmy had served part of a life sentence for murder. The killing was of an old man and took place in the course of a robbery; she assumes that neither of her grandfather's wives ever knew about his conviction. This is the first shock. Then she travels to South Africa to continue her research in the national archives in Pretoria and to meet her mother's extended family, and the shocks come thick and fast.

On interviewing Paula's siblings, whom she had only previously heard about in her mother's filtered version of her childhood, Brockes discovers that Jimmy was a violent alcoholic who sexually abused three of his four daughters, beginning with Paula. The latter decided to take legal action against him when she realised that he had begun to have regular intercourse with her 12-year-old sister, and her other attempts to stop the abuse (which included trying to shoot him when he came home drunk one night) had failed. A guilty verdict seemed imminent when Paula's stepmother withdrew her testimony. The case collapsed and Jimmy returned to the family home. Paula – who had borne the situation for years in order to protect the younger children – considered suicide. Her relocation to England was a bid to save her own life. By a twist of fate, her father died of an aneurism while she was making the crossing.

The Pretoria archives yield the trial transcripts in all their merciless detail, but Brockes wisely keeps back excerpts from these until the end. Her objective is not to write a misery memoir but to foreground her mother's astonishing resilience, which the naked facts might otherwise obscure. Brockes handles her toxic material with a lightness of touch that navigates skilfully between tragedy and bleak comedy, not least in her impressions of her newfound family. Her uncles are hard-drinking men with a violent streak; one is an evangelical crackpot living in a garage, another a reclusive therapist who has retreated to the bush. Her aunts, Faith and Doreen, are superficially brassy but contused underneath. Faith – whose repeated rape by Jimmy prompted Paula to take action – has no memory of these incidents or the trial. "Remembering on that occasion got her nowhere," reflects Brockes. "She has every right to remember nothing." Doreen, on the other hand, recalls an attempt by Jimmy to assault her when she was five: "I screamed so loudly … And I'm still screaming now."

Though Brockes is appalled by the distance between the home counties mother she knew and the deprivation of Paula's childhood, the pathos of the disclosure is leavened by gallows humour. Her uncle Tony recalls their upbringing in a house without electricity or running water, from which their father's nightly drunken rages would drive the family to take flight: "I'd see Mom fly past, then Faith, Doreen, Steven, Barbara, your mom, John, out of the window, over the barbed-wire fence, over the next fence into the veldt and under a thorn tree. We'd wake with frost on the grass, shit between our toes … Your mom got up and dusted herself off. 'We may be poor,' she said, 'but we sure see life.'"

It becomes poignantly clear that the care of this gallant older sister allowed the others to survive. As Tony admits, "You can endure so much – violence, poverty – if there is love. Paula loved us." Brockes, too, experienced her mother as loving, tough and full of joy. Just how loving she was can be gauged by her determination not to burden Brockes with her suffering. All the indications are that, unlike Faith, Paula remembered her abuse by Jimmy perfectly well, but decided not to give it a place in her own daughter's life. It seems that this was not an act of repression, but of extraordinary selflessness. Brockes notes that shortly before her death her mother remarked of her childhood, "I think I have come to terms with it." "Not 'came', but 'come'. As if, in all those years of village life, in the market, at the tennis club, in the midst of our mild existence, a process had been ongoing, another reality alive to her in which she'd been wholly alone."

By any reckoning, Paula at last achieved an outward life of placid security worthy of that dinner service in her trunk. What about the gun, the one with which she'd tried to shoot her father? In fact, she surrendered it to the police decades after arriving in England. But she did not need to leave her daughter a gun in the end. Her real bequest to Brockes was the psychological freedom to be able to confront the past without inhibition, and to take straight aim at it. The gun is this book.

• Elizabeth Lowry's The Bellini Madonna is published by Quercus.