Not long before Hafez el-Assad died in 2000, Ahmed Hariri predicted what would happen when the official news announced the death of the president. Hariri, an old friend of mine in the Syrian ministry of information, came from the city of Tadmor, east of Damascus. The city, known as Palmyra to Romans and tourists alike, was home to one of the regime's fearsome jails, which stood behind trees not far from the desert road to Baghdad. This was the site of a massacre of Islamist prisoners – perhaps a thousand in all – by Assad's brother Rifaat after an assassination attempt on Hafez. The corpses were rumoured to have been tossed by night into a secret mass grave near a local hill, and have lain unmarked ever since.

Hariri – he died some years ago, which is why I can name him – drew heavily on a cigarette in the back of my car as we sped towards Tadmor. "When our beloved president dies," he said, "all the people of Tadmor will go to the hill. They know where the dead are – more than just those killed by Rifaat. And when they are sure that the president has gone, they will all throw roses on the gravesite in memory of those who lie beneath."

But when Assad died of a heart attack, and a smooth Baathist succession installed his son Bashar as the president, not a soul walked from Tadmor to the mass graves. There were no mourners, no roses, no recognition of the violence that had stained this terrible prison under Assad's 30-year rule.

The eventual relief of Syrians that the young English-trained optometrist Bashar – a gentler figure than his ferocious father – had taken over was so great that no-one wished to recall the past. Why dig up a mass grave unless you intend to pour more blood into it?

The subsequent rule of Bashar has not produced the democratic "spring" in Syria which many Arab intellectuals had hoped for, a fact made all too clear in a report published in Washington this month by the Transitional Justice in the Arab World Project, supported by Freedom House. According to the report, Years of Fear, as many as 17,000 Syrians may have been "disappeared" during Hafez el-Assad's rule; the 117-page document contains heart-breaking accounts of disappearances and extra-judicial executions, and descriptions of the apparently vain 30-year wait of sons, wives and parents for the return of men who were almost certainly killed in the early 1980s.

But all such reports should carry a red flag. Freedom House, which last year labelled Israel as the only "free" country in the Middle East (Lebanon got a "partly free" coding), receives around 66 per cent of its funding from the US government, including the State Department and USAID. Its roots go back to 1941 – Eleanor Roosevelt was one of the first sponsors when Freedom House was pointing up the evils of Nazi Germany. In the past it has been accused of supporting only pro-Western opposition movements, but its Middle East targets have largely been Arab. Freedom House was also previously led by James Woolsey, a former director of the CIA.

Radwan Ziadeh, who compiled the report, is a long-time US resident exiled from Syria for many years. He runs the Damascus Centre for Human Rights Studies. This does not disqualify his report, but he warns readers in his preface that "for security reasons, we withheld the names of those interviewed and have changed some facts to disguise their identities. Similarly, we have scrambled [sic] the details of many human rights activists and former detainees whom we interviewed." This does not, to put it mildly, bestow total confidence on the report. The Syrian authorities will no doubt seize upon this to debunk its contents. So, reader, you have been warned.

Years of Fear covers the three-decade rule of Hafez el-Assad, Syria's former air force commander whose long battle to maintain his Alawi rule and whose ferocious struggle against violent Islamist enemies clogged the fetid prisons of Syria with thousands of political prisoners. Using security forces who were often corrupt, he confronted an ever more violent sectarian guerrilla movement whose first major assault came on 16 June 1979 when an army captain, Ibrahim al-Yusuf, led the massacre of Alawi students at the Aleppo artillery school.

A subsequent assassination attempt on the president prompted Rifaat's Defence Brigades' assault at Tadmor in which up to a thousand Muslim Brotherhood prisoners were machine-gunned to death in their cells. By 1980, there was open war between the regime and its opponents. Law 49, of 7 July 1980, mandated capital punishment for those who did not renounce their Brotherhood membership in writing, and a Ghadaffi-style assassination campaign against overseas opponents was ordered.

The Hama uprising in February 1982, in which the old, rebel-held city was virtually destroyed by tank and shell-fire, caused up to 15,000 deaths, according to Ziadeh's report – some put the figure at 20,000. What Ziadeh oddly fails to mention is the underground fighting in Hama in which girl suicide bombers hurled themselves against Syrian troops, and previous violence in the city in which Islamists slaughtered entire families of Baath party officials. There was nothing exclusive about Syria's mass-murderers.

Ziadeh believes that in the early Eighties and later, up to 25,000 men went missing, swallowed into interrogation centres and prisons. "Most such cases occurred before 2000," the report says. "Many detainees have been released during the past few years." A credit to Bashar al-Assad, no doubt.

But in the years before, there was no such compassion. The report quotes a former detainee at Tadmor. "They called on groups of brothers every Monday and Thursday, and executed them by hanging in the courts of Palmyra Prison..." It is a sign of the Middle East's endemic cruelty that Saddam Hussein's regime was infinitely worse than Assad's.

Other Syrian detainees might be sentenced to a short term of imprisonment, then held for 10 years, their families repeatedly told that none of the security agencies had any knowledge of them. "Now," Ziadeh writes with teeth-sucking restraint, "the family is allowed to visit the detainee after several years of detention."

Ziadeh is at his strongest when he lists the vast legislative shield which is supposed to protect Syrian citizens from arbitrary arrest, torture or execution. Section 3 of Article 28 of Syria's constitution, for example, states that "no one may be tortured physically or mentally or be treated in a humiliating manner." A double irony – one which, again, Ziadeh fails to mention – is that the American government, which supports Freedom House, happily renditioned prisoners to Damascus in the sure knowledge that the Syrians would ignore their constitution and torture the suspects to their heart's content. Another Syrian law says that the state must "take the necessary legislative, administrative, and judicial measures to prevent and terminate acts of enforced disappearance."

Again, Ziadeh uses the published evidence of Abdullah al-Naji to prove that the ruthless "field courts" adopted by the regime – an institution originally set up to deal with the Israeli "enemy" rather than Syrian "enemies" of the Baath party – were run by Ghazi Kenaan, the former head of Syrian army intelligence in Lebanon and later minister of interior. I knew Kenaan – a jovial, frightening man who once helped me escape Beirut's kidnappers by asking me to join him on his morning run across west Beirut; he later committed suicide after allegedly plotting, as minister, against Bashar al-Assad.

But Kenaan's command of the "field courts" makes sense. More than 15 years ago, in a Boston hotel, another Syrian held at Tadmor told me that they knew when executions were about to take place. "We would stand at the cell windows and we all knew Kenaan's favourite aftershave. When we smelt it, we knew there were going to be firing squads." Of these executions, the report comments that "no one knows where those who were executed or died under torture were buried."

The report suggests that these disappearances indirectly affect up to a million Syrians – five per cent of the population. Amer, who was eight when his father was arrested, recalled: "I cannot speak with anyone about the issue of my father, because this induces fear and makes people suspicious... I have lived as a half orphan, although my father is not officially dead."

Some men were declared dead – and then reappeared alive, like the 16-year-old arrested in Aleppo who spent 14 years in prison. Ziadeh's report, which contains some obvious errors – one woman speaks of her arrested son who, later, mysteriously turns out to be her father – makes the point that "victims and their families ... have an inalienable right of knowing the truth about the circumstances in which violations took place and about the fate of the victim in the case of death or disappearance."

A human rights activist told Ziadeh that in some cases buildings were erected over secret cemeteries. In Aleppo, a large mosque has allegedly been built over a mass grave.