A few hours after the ferocious attack on Damascus by the Free Syrian Army began last month, the new Syrian minister of information, Omran Zouhbi, turned on journalists in the capital. "What are you doing here in Damascus?" he roared. "You should be out with our soldiers!" And within a day, tired images of a primly smiling President Bashar al-Assad and pictures of Syrian troops happily kissing children were replaced by raw – and real – newsreel footage of commandos fighting their way across Baghdad Street under fire from the rebel opponents of the regime, grimy-faced, running from street corners, shooting from the cover of walls and terraces. "We've cleaned up here," one tired but very angry officer said. "So now we're going to get the rest of those bastards." Never before – not even in the 1973 war when the Syrian army stormed Observatory Ridge on the heights of the Golan – had the Syrian public witnessed anything as real as this on their television sets.

And – despite all the mythical tales of its presence in every smashed village – the battle for Damascus really was fought by Maher al-Assad's ruthless 4th Division. The soldiers loyal to Bashar's younger brother gave no quarter. "It was a slaughter, a massacre," a Syrian with expert knowledge of the military told me. "A lot of the corpses were already bloated within hours, but you could tell some of them weren't Syrian; there were Egyptians, Jordanians, Palestinians, one Turk, Sudanese …" He counted 70 bodies at one location, 42 of them non-Arab. The FSA said it lost only 20 men, and claimed that the Syrians emphasised the number of "foreign fighters" they found among the dead. "Syrian soldiers don't like to think that they are shooting at fellow Syrians – they feel much more comfortable if they believe they are shooting at foreigners," the young man said.

The statistics of the Syrian war will always be in dispute – both sides will minimise their losses while they are fighting and exaggerate the number of their "martyrs" once the conflict is over; nor will we ever know the true number of the civilian dead, nor the exact identity of their killers. Given unprecedented access last week to majors and generals whom the West accuses of war crimes, I found only one officer who would partially admit the existence of the murderous shabiha militia credited with atrocities in largely Sunni Muslim towns and villages. "The shabiha doesn't exist," he told me. "It is a figment of imagination. There are village 'defenders' who guard some areas …"

And that, of course, is exactly what the shabiha claim to be, local Syrian civilians protecting their homes from the government's enemies. They existed in Algeria during that country's barbaric conflict between the dictatorship in Algiers and the Islamist rebels in the 1990s, protecting their families while committing atrocities in towns and villages believed to be used by – or sympathetic to – their "terrorist" Muslim enemies. In Algeria, too, the government's opponents were called foreign fighters, men who had fought in the Afghan war against the Russians and who had returned to continue their holy war against the secular regime in France's former colony. Now another former French colony's secular – albeit Alawite-dominated – leadership says it is fighting men from Afghanistan, making no distinction between Unity Brigades or Muslim Brothers or Salafists or just plain Free Syrian Army. No one will be surprised to learn that there has always been the closest military-intelligence relationship between Algiers and Damascus.

But the government army's battle with its Syrian and foreign antagonists has not always gone as smoothly as the regime would like the world to believe. Despite the narrative now peddled in the West, armed men were present on the streets of Syrian cities and villages since the very early days of the Syrian awakening 18 months ago. True, the Arab Spring initially took the form of demonstrations by tens of thousands of unarmed protesters in the great cities of Syria, but an Al Jazeera camera crew captured film of gunmen attacking Syrian soldiers near the village of Wadi Khallak in May 2011. That same month, Syrian television obtained tape of men armed with Kalashnikovs near crowds of unarmed Syrian protesters in Deraa, where the revolt began after secret police officers tortured to death a 13-year-old boy.

Yet when they first entered Deraa, it appears, Syrian officers and their soldiers did not themselves believe they were facing armed opponents. "Sixty per cent of the city was secured by us in just one day," a Syrian familiar with the operation says. "We sent in only 1,100 soldiers – this would never happen now – because they did not think there were any armed groups there. But by the time we had recovered the rest of the city in the next five days, we had lost 17 of our men dead to sniper fire." This was not the only surprise: once pitched battles began later in the year, the Syrian military was amazed by the firepower of its opponents.

"In Homs, the army was inside a building that received hundreds – literally hundreds – of rocket-propelled grenades," a Syrian familiar with the operation says. "There were thousands of explosions, and eventually we had to evacuate the entire building because it was going to crumble. When the soldiers were out, they had to explode the whole place before it crashed to the ground." And for an army condemned for its own cruelty in battle, the Syrians were astonished by the ruthlessness of those opposed to them.

In Andan, a heavily defended army checkpoint was wiped out last year when the Liwa Tawhid, the Unity Brigade, assaulted the position and killed all 75 soldiers and four officers. In a later ambush at Shughour, 120 soldiers were killed. Army files record nine security officers murdered at a police station at al-Hadr in Hama province, eight policemen at another office in the same province. In Salkin, another town in Hama, an ex-army civilian lorry driver employed by the Army's Vehicle Service Station 5036 was assaulted by civilian crowds. Abdul Fatah Omar Abdul Fatah was accused of being a member of the shabiha, stripped naked and hanged, then his corpse was pelted with shoes and decapitated. In Duma, a mosque leader told worshippers: "Among us, there is an Awaini," – a traitor. The man was beaten to death. His name is recorded as Abu Ahmed Akera.

When the Free Syria Army followed up its attack on Damascus with an assault on Aleppo, the authorities found that the first target of their enemies was the artillery school. More than 70 cadets managed to resist until reinforcements reached them. Word has it that all anti-aircraft missile crews at the school were hastily taken out of Aleppo to save them from capture and help protect the country's tactical missile defences from possible Israeli or Nato attack.

Syrian soldiers fighting their way through the winding, narrow streets of Aleppo's old city this week might choose to remember a young Egyptian student who spent months in Aleppo in the 1990s, working on an urban planning thesis that included the very battlefield in which the army is now fighting: Mohamed Atta, the leader of the 9/11 hijackers in the US. Some of the attacks on Syrian officials have been planned with great care; scientists at the Scientific Research Centre outside Damascus have been murdered. Long before the air force was first used in the war – the army claims this was in June – seven pilots were killed by rebels last year. The military says that it began using artillery – as opposed to mortars – only in February.

For the government, the outlook appears harsh. The army believes Idlib – reported to be an al-Qa'ida stronghold – will be one of the most critical battles in the war. There are reports of fearful conscripts seized from a civilian bus in central Syria and given an option: either their parents hand over 450,000 Syrian pounds (£7,000) to the Free Syrian Army or the young men must join the rebels. In the village of Rableh near al-Qusayr, a largely Christian population of 12,000 is said to be held hostage by rebels as human shields, although the army has apparently decided it would be too costly to take the village.