President Assad's army is starting to call the shots in Syria

Old Mohamed Said al-Sauda from Deraa, in his tawny gown and kuffiah headscarf, sat at the end of a conclave of tribal elders, all newly arrived in Damascus for an audience with no less than the President himself. They sat – only one woman in a blue dress among them – round a long table in the Damas Rose Hotel drinking water and coffee, rehearsing their anxieties. How should they talk to the young armed men who came into their villages? How should they persuade the rebels not to damage their land and take over their villages? "We try to talk to the saboteurs and to get them to go back to rebuilding the country," al-Sauda told me. "We try to persuade them to put aside their arms, to stop the violence. We used to have such a safe country to live in."

These men, middle-aged for the most part with tough, lined, dark faces, are the first line of defence of the Assad regime, the landowners and propertied classes of the peasants who benefited most from the original Baathist revolution and whose prosperity has been threatened by the mass uprising against the regime. They come from Tartus, Deraa, the Damascus countryside, from Hama and Latakia, and they speak the language of the Assad government – up to a point. "Syria is a mosaic unlike any other in the world," says Salman Hamdan. "The sectarian divide does not exist in our country. Muslims, Christians, they are the same. It is a conspiracy that is classifying people. Some have chosen the homeland; others have decided to be ungrateful to their country for personal gain."

But the woman in blue hands me a printed sheet of paper with a list of demands. "We come from all walks of political life," it begins. "We reject violence and we reject repression, sectarian massacres and the destruction of the cultural heritage of Syria." And there it was. That word. Repression. For these men and this lonely woman know what helped to set fire to Syria. "Every government makes mistakes," one of the men says – but we know what he means. He is talking about the mukhabarat intelligence service which lit the fire two years ago by its brutality towards the children of Deraa. The system of torture and fear that the secret police services of the regime imposed for decades upon Syria – the "repression" mentioned so obliquely in the lady's demands – still lies like a blanket over those areas of the country that the government still controls.

How does a Syrian loyal to the regime tell its leader that his own security agencies helped to bring down this catastrophe upon their country? For these agencies have contaminated not just the Baath and the President but even the government army – the Syrian Arab Army – which is now trying to shrug off the awful carapace of legimitised violence that the plain-clothes men, in their tens of thousands, have used as a tool for more than 30 years. Even in the cities that the government still controls they have still not learned their lesson.

A clerk at the "Terrorism Tribunal" in Damascus admits that 1,000 new files go into the court every day – a huge figure that only hints at the vast numbers of unknown prisoners in the regime's jails. But the figure is also, in the words of one well-placed Syrian, a "chequing account", a bank balance of fear that rises and falls according to the security searches and arrests. If 1,000 are arrested today, another 1,000 can be released tomorrow. The state security organs now appear to restrict themselves – if that is the right word – to arresting only those whom they believe are an immediate danger to themselves, to Assad or to the regime. They no longer have the time or resources to hunt down every protester. Nor do they have any longer the vast territory of the countryside in which to roam.

There are also some intriguing signs that the government army, so keen to appear as the foundation stone of the state – which it is – without the dark stain of fear left by the mukhabarat, is taking its own steps to push back the "terror" men. The military security forces, now that they have – for the first time – to deal directly with their own civilians, are giving orders over the heads of the intelligence agencies. In 2010, Assad himself took a decision to ban security agents from carrying weapons covertly – a highly contentious rule for the secret police – and the army has now followed on from this.

The army, for example, is today in command of security in battle. In the past, military intelligence men would give instructions to the army. But the Syrian army is now in charge. Field commanders – not cops – make decisions. There have been many cases, according to those involved with the military, where plain-clothes security agents witnessed brutalising civilians have been arrested and – incredibly – put before military courts. The generals and the colonels, in other words, are no longer prepared to play patsy to the regime's thugs.

But romantics beware. The army is a ruthless machine and its commander-in-chief remains Bashar al-Assad. Its loyalty is still without question. The UN maintains voluminous files of war crimes that they say were committed by regular soldiers in the Syrian army. And the idea that the presidency itself may abandon its own security agents is a myth. A militarised state will always need a bodyguard of secret policemen. Nor will Assad's enemies ever accept an army takeover – with or without an Assad leadership – as a compromise for a truce. For them – correctly – the army remains more dangerous than Assad himself. The mukhabarat may come and go, but the army remains.

There are stories in Damascus – and here you must float on the wings of all kinds of black and white doves – that the army leadership is distancing itself from the thugs of air force security and from the infamous 4th Division of Maher al-Assad, the president's brother. When all 45 soldiers are killed in every checkpoint surrounding just one rebel suburb of Damascus – as happened three months ago – commanders must make their own decisions. And now that so much of the countryside has been lost to the government, the army's role in the cities has increased.

It is an irony of Syrian history that hitherto most threats to the regime have come from within the cities. The Muslim Brotherhood, still officially illegal in Syria, was an urban institution and it was the Brotherhood that threatened Damascus and the central cities of Homs and Hama in the 1980s. The great uprising of 1982 emanated from the centre of Hama, from the city's mosques and underground tunnels; and thus the cruellest of the nation's security forces, the Special Forces of Rifaat al-Assad – led by the president's now-disgraced uncle – was sent in to liquidate the Brotherhood and up to 20,000 of Hama's residents. But now the uprising comes from the countryside, the defectors of the Free Syrian Army and the al-Nusrah and the various Islamist outfits – with their clusters of foreign jihadis – who are moving in from the villages and descending on the cities. The agrarian refugees already in the cities have thus joined the rebel forces – which is why the normally secure government city of Raqaa fell so swiftly on 4 March.

That a regime originally founded on peasant reform should discover that its enemies now live among that same peasantry is a terrible stroke of history for Baathism. That a nation with a non-sectarian constitution – needless to say, we all know what is wrong with it – should find itself consumed by the very sectarian conflict that it was designed to prevent is a tragedy. No wonder the new 60-man special units of the government army being trained for operations across Syria are a careful mixture of all sects – Sunnis, Christians, Alawis, Druze and others – and are openly referred to as the most "colourful" of all military battalions. This may be intended to improve their image in what is left of "public opinion". But it is also a faint ghost of what some army officers hope a future Syrian army may be.

For the message – if there is one in the coming weeks and months – is that the most important institution to watch in Syria is not the regime. Nor is it Bashar al-Assad. Nor is it the secret police. Nor is it the Free Syrian Army, nor al-Nusrah. Nor the platitudes of the White House or Downing Street. It is the government Syrian Arab Army. Watch, as they say, this space.