The priceless treasures of Syria's history – of Crusader castles, ancient mosques and churches, Roman mosaics, the renowned "Dead Cities" of the north and museums stuffed with antiquities – have fallen prey to looters and destruction by armed rebels and government militias as fighting envelops the country. While the monuments and museums of the two great cities of Damascus and Aleppo have so far largely been spared, reports from across Syria tell of irreparable damage to heritage sites that have no equal in the Middle East. Even the magnificent castle of Krak des Chevaliers – described by Lawrence of Arabia as "perhaps the best preserved and most wholly admirable castle in the world" and which Saladin could not capture – has been shelled by the Syrian army, damaging the Crusader chapel inside.

The destruction of Iraq's heritage in the anarchic aftermath of the Anglo-American invasion of 2003 – the looting of the national museum, the burning of the Koranic library and the wiping out of ancient Sumerian cities – may now be repeated in Syria. Reports from Syrian archeologists and from Western specialists in bronze age and Roman cities tell of an Assyrian temple destroyed at Tell Sheikh Hamad, massive destruction to the wall and towers of the citadel of al-Madiq castle – one of the most forward Crusader fortresses in the Levant which originally fell to Bohemond of Antioch in 1106 – and looting of the magnificent Roman mosaics of Apamea, where thieves have used bulldozers to rip up Roman floors and transport them from the site. Incredibly, they have managed to take two giant capitols from atop the colonnade of the "decumanus", the main east-west Roman road in the city.

In many cases, armed rebels have sought sanctuary behind the thick walls of ancient castles only to find that the Syrian military have not hesitated to blast away at these historical buildings to destroy their enemies. Pitched battles have been fought between rebels and Syrian troops amid the "Dead Cities", the hundreds of long-abandoned Graeco-Roman towns that litter the countryside outside Aleppo, which once formed the heart of ancient Syria. Syrian troops have occupied the Castle of Ibn Maan above the Roman city of Palmyra and parked tanks and armoured vehicles in the Valley of the Tombs to the west of the old city. The government army are reported to have dug a deep defensive trench within the Roman ruins.

"The situation of Syria's heritage today is catastrophic," according to Joanne Farchakh, a Lebanese archaeologist who also investigated the destruction and plundering of Iraq's historical treasures after 2003, and helped the Baghdad museum to reclaim some of its stolen artifacts. "One of the problems is that for 10 years before the war, the Syrian regime established 25 cultural museums all over the country to encourage tourism and to keep valuable objects on these sites – many placed stone monuments in outside gardens, partly to prove that the regime was strong enough to protect them. Now the Homs museum has been looted – by rebels and by government militias, who knows? – and antique dealers are telling me that the markets of Jordan and Turkey are flooded with artifacts from Syria."

There is, of course, a moral question about our concern for the destruction of the treasures of history. Common humanity suggests that the death of a single Syrian child amid the 19,000 fatalities of Syria's tragedy must surely carry more weight than the plundering and erasure of three thousand years of civilisation. True. But the pulverisation and theft of whole cities of history deprives future generations – in their millions – of their birthright and of the seeds of their own lives. Syria has always been known as "the Land of Civilisations" – Damascus and Aleppo are among the world's oldest inhabited cities and Syria is the birthplace of agrarian society – and the terrible conflict now overwhelming the country will deprive us and our descendants of this narrative for ever.

To their enormous credit, Syrian archaeologists have themselves anonymously catalogued the destruction of their native country's historical sites. They include government shelling of villages that exist within ancient cities; rebels have apparently been sheltered, for example, in the small civilian township built inside the wonderful ruins of Bosra which contains one of the best-preserved Roman theatres in the world – which did not prevent several buildings from being destroyed. Similar bombardments have smashed the fabric of Byzantine-era buildings in al-Bara, Deir Sunbel and Ain Larose in northern Syria.

In the monastery of Sednaya, apparently founded by the Emperor Justinian – the people of the village still speak Aramaic, the language of Jesus – shellfire has damaged the oldest section of the building, which dates back to 574. The Umayyad Mosque in Deraa, one of the oldest Islamic-era structures in Syria, built at the request of the Caliph Omar Ibn al-Khattab, has also been damaged. Dr Bassam Jamous, the government-appointed director general of antiquities in Syria, says that "terrorists" – ironically, the Western world's own nomenclature for state enemies – have targeted historic buildings in Damascus, Aleppo, Bosra, Palmyra and the Citadel of Salah al-Din (Saladin), a crusader fortress seized by the Kurdish warrior hero in 1188, the year after he recaptured Jerusalem for the Muslims from Balian of Ibelin.

Several months ago the Syrian authorities reported the theft of the golden statue of an 8th century BC Aramaic god – still unfound, although it was reported to Interpol – and admitted thefts at government museums at Deir ez-Zor, Raqqa, Maarat al-Numan and Qalaat Jaabar. Hiba Sakhel, the Syrian director of museums, has confirmed that items from the Aleppo museum have been transferred to the vaults of the central bank in Damascus for safekeeping.

"Syrian Archeological Heritage in Danger", a group of Syrian specialists who list the destruction and looting of the country's treasures on their own website, has revealed that Syria's Prime Minister, Adel Safar, wrote to fellow ministers on 11 July last year warning that "the country is threatened by armed criminal groups with hi-tech tools and specialised in the theft of manuscripts and antiquities, as well as the pillaging of museums". The archaeologists find this note "very odd" because it appears to warn of looting which had not yet occurred – and thus suggests that officials in the regime might be preparing the way for their own private theft and re-sale of the country's heritage, something which did indeed occur under President Assad's father Hafez al-Assad.

So the looting and destruction lies at the door of all sides in the Syrian conflict, along with the thieves who move in on all historic sites when the security of the state evaporates. In truth, Syria has always suffered – and the regime always tolerated – a limited amount of theft from historical sites, to boost the economy in the poor areas in the north of the country and to enrich the regime's own mafiosi. But what is happening now is on an epic and terrifying scale. "As for the old churches, old houses, old streets of Homs, you can forget it – they don't exist any more," archaeologist Joanne Farchakh says. A specialist in heritage in times of war in Lebanon, Iraq and northern Cyprus as well as Syria, she gloomily reports new information from the second millennium BC sites in which looters have dug huge holes, metres wide, to unearth the treasures of pre-history.

Much of this destruction is taking place not only in the world of ancient Rome, the Crusaders and the Muslim conquest and revival, but in the land of the original "terrorists", the Assassins whose murderous attacks on all authority a thousand years ago were led by "the Old Man of the Mountains". He once besieged Al-Madiq castle – whose bombardment by the Syrian army is now available on videotape.

As old as war itself

Maybe we "Westerners" have a bit of a nerve to denounce the destruction of Syria's antiquity. From the Roman destruction of Carthage to RAF Bomber Command's pounding of Hamburg, Dresden and a hundred medieval German cities to rubble, we have been smashing our history to bits for centuries. The pillaging of Europe's great cities was a practice of war as common as the rape of an enemy's womenfolk for hundreds of years, and the last century has witnessed such savagery on an unprecedented scale. The German destruction of the Louvain library and the Cloth Hall of Ypres and countless French Gothic cathedrals and churches in the First World War, to the bombing of Rotterdam, the City of London, Coventry and Canterbury and the great cities of Germany – not to mention the priceless monastery of Monte Cassino – we are in no position to point the finger at the Arab world for its historical self-immolation.

In Croatia and Bosnia in the early 1990s, I saw the same thing. The pulverisation of mosques and Catholic and Orthodox churches, the smashing of gravestones – even the bulldozing of graveyards – were a form of cultural cleansing that reached its apogee in the burning of the old Sarajevo library. In Baghdad in 2003, hired mobs smashed into the National Museum and took the treasures of Mesopotamia. I crunched my way across the floor on fragments of Greek statues which were of no interest to the looters, and then watched the burning of the Koranic library, the flames of 15th-century Korans too bright for the naked eye. I rescued just a few 18th-century Ottoman documents flapping in the breeze down outside.

Some of these destroyers were brought into the city by bus – I saw them climb back aboard outside the library and identified one of them at another burning – and it is true that most cultural destruction is organised. Looters come in armies. Joanne Farchakh and I visited the legions of thieves working in the Sumerian sites of southern Iraq as they hurled priceless second millennium BC clay jugs out of their troglodyte holes in order to reach older, fourth millennium treasures at a greater depth. During the Lebanese civil war, looters in southern Lebanon would offer me Phoenician gold bracelets from the ancient cemeteries around Tyre. No one knows how many treasures Lebanon lost between 1975 and 1990. In 1975, the Syrian army – just as they have done today – based soldiers in Lebanon's historical sites, including the temples of Baalbek in the Beqaa Valley. The Temple of Jupiter still bears the scar of a Palestinian RPG in its south-west corner.

This is why it is so important to have an inventory of the treasures of national museums and ancient cities. Emma Cunliffe, a PhD researcher at Durham University, published the first detailed account of the state of Syrian archeological sites in her Damage to the Soul of Syria: Syria's Cultural Heritage in Conflict, listing the causes of destruction, the use of sites as military positions and what can only be called merciless looting. Much of her work has informed the studies of archaeologists like Farchakh.