In 2008, Judge Baltasar Garzon opened an inquiry into crimes against humanity committed by General Franco's forces and sympathisers during the civil war, and by his regime in the following years.

In 2010, egged on largely by right wing groups, the Spanish Supreme Court indicted Garzon for violating a 1977 law that had pardoned all such crimes and issued a general amnesty in the name of national recovery. After two years of hearings, Garzon was finally acquitted – just ahead of the publication of The Spanish Holocaust, and one week before the Spanish translation. Paul Preston's extraordinary work is by far the most detailed – and damning – account to date of those atrocities.

Preston is the most respected historian of the Spanish civil war and, as a biographer of Francisco Franco, of the brutal years that followed. His latest work is a monumental piece of research. In page after page, he offers grim – if elegantly and thoughtfully written – proof of atrocities, crimes and cover-ups committed in the name of political dogma and convenience. I use the word proof deliberately: there can be no doubting Preston's scholarship, nor his meticulous checking of facts, documents and oral testimony.

"Behind the lines during the Spanish civil war", Preston begins, "nearly 200,000 men and women were murdered extra-judicially or executed after flimsy legal process." That figure does not take into account the murders and executions that continued after the war. Despite the stupefying figures, Preston worries about using the word "holocaust" in the title. He argues his case convincingly, not only in terms of numbers and in the cold-blooded "practical" way in which the killings were carried out, but in that much of the bloodbath was justified by a deep anti-Semitism. The slaughter of innocent Spaniards was legitimised by Falangists by a need to exterminate "the instruments of a Jewish-Bolshevik-Masonic conspiracy".

I work regularly in Pamplona, a region that fell quickly and enthusiastically to Franco's rebels. A group of us go out on a Saturday night for tapas and "vinos" in the old part of town. There are two bars, however, that we always pass by, and I wondered why – they both look very inviting. An awkward conversation ensued by the end of which I got the idea (but was not told directly) that those bars are still associated both with the war rebels and with the Regime. Nearly 80 years later social life is still divided.

Nobody in Pamplona talks much about their parents and grandparents and what they got up to during the war. The Garzon trial has divided them, and not just along the old deeply embedded Republican/Francoist lines. A high percentage of Spaniards believe that crimes of the past should be punished, but just as many fear opening up the past.

And the past is complex. Preston does not confine himself to the violence and injustice of the rebel generals and their sympathisers. The Spanish Holocaust examines just as scrupulously the crimes and excesses perpetrated in the Republican zone during the war against anyone suspected of colluding with the generals. But "popular justice" was sometimes a facade behind which common criminals, or fanatical footsoldiers justified acts of cruelty, greed or revenge.

In areas of Spain where anarchism was strong – most notably Catalonia – the situation gets messier still. Preston picks his way through the morass of competing interests within the Republican camp – anarchists, communists and nationalists battling it out for superiority.

The killing of priests and sacking of churches at the outbreak of war to this day triggers furious argument: who really did the killing and who takes the blame? Preston has delivered the most accurate balance sheet to date. If anything, he downgrades the activities of the anarchists and their allies, both in the numbers of deaths attributed to them, and their effect on the final outcome of the war. With the sheer academic precision of its research this book will not only have an immediate legal impact, but give grist to the mill of a debate that will continue to grind for years to come.

In the cold mathematics of the war, the slaughter was of a different order on the rebel side. Preston writes that "the differences between the numbers of deaths at the hands of the Republicans and at the hands of the rebels are shocking".

Though every page of The Spanish Holocaust is necessarily dripping in blood, Preston never loses sight of the human perspective and, through his exhaustive knowledge of the era, he explains the most labyrinthine politics and events. Not everyone will agree with everything he concludes – least of all those who will doubtlessly continue to campaign for Judge Garzon's conviction – but Preston has undoubtedly produced one of the most important documents of modern history.

Paul Preston is at Aye Write! festival on March 17 at 5pm. To book tickets, call 0141 353 8000, or visit www.ayewrite.com.

The Spanish Holocaust

Paul Preston

Harper Press, £30