Wasid, a Syrian conscript, set off for the southern town of Deraa in late April filled with the zeal of a soldier going to war. "We were going to fight terrorists," he said. But less than a day after arriving there, he was planning to defect.

The Syrian regime has cast the uprising in Deraa as a conflict between a loyal military and a large and highly mobile group of heavily-armed foreign-backed insurgents, roaming the country attempting to ignite sectarian strife.

Over three hours in an Istanbul safehouse, Wasid, 20, described events in the southern town where the wave of dissent that has swept Syria first broke. His account starkly contradicts the official narrative.

"As soon as we got there, the officers told us not to shoot at the men carrying guns. They said they [the gunmen] were with us. I couldn't believe what I was hearing. It had all been lies," he said.

In the month they were stationed there, neither Wasid nor any of his colleagues saw any demonstrators with weapons in Deraa or the nearby town of Izraa. And instead of confronting armed insurgents, the unit was ordered to shoot protesters. "It shocked me," he said. "We are soldiers and soldiers do not shoot at civilians."

In the weeks leading up his deployment with the Syrian army's 14th Division, commanders had given regular briefings on the "violence" ahead. Wasid was convinced he would soon be in combat.

"When we were at the base in Damascus before we left for Deraa, we were not allowed to watch television at all, except for two hours each day when we could watch Rami Makhlouf's channel," he said. [Makhlouf, a tycoon, is President Bashar al-Assad's first cousin]. "All they showed were armed groups roaming the villages. I found out later that these groups were on our [the regime's] side – they were the Shabiha." According to Wasid, the Shabiha – ghosts – were the only civilian gunmen in town. Their group has strong links to the military and has developed a reputation over recent bloody months of being willing to do the dirty work in troublesome towns and villages.

"The first day we arrived there, 24 April, the Shabiha came to the base to speak with our officers. It was clear that the relationship was close."

Wasid showed the Guardian his military ID and application for refugee status, copies of which have been kept.

He does not want his real name or photograph used out of fear that his family may be targeted for reprisals.

After weeks of military crackdowns, the government is now on a diplomatic and media offensive. Officials are pushing their version of events to a few correspondents who were last week allowed to enter Syria for the first time since March. The official account has emphasised claims that Sunni Islamist groups have either initiated or hijacked the uprising's agenda.

"I never saw an Islamist or anybody that resembled one," said Wasid. "And nor did anyone else with me."

He estimated that about 30% of his unit were disaffected with the military.

But neither dissent nor defection are easy in Syria, where conscripts are paid £6 a month. "One guy – I only know his name as Wael, he was from the east – told an officer that what we were doing was wrong. "The next day he was killed. They said he had been shot by terrorists." Nevertheless, by 25 May Wasid and 20 others had mustered the courage to attempt to escape. He ditched his military fatigues – and the sniper rifle which he said he had never used – and ran with the group to the highway, where a van took them to Damascus. "Once we got there, we agreed we would go separate directions. I stayed in Damascus for three days and then left for Turkey. I don't know where the others went."

He crossed the border in the Kurdish northeast of Syria and made his way by bus to Istanbul, where the UNHCR and rights group Avaaz are helping him. Wasid's testimony will be used in a referral to the international criminal court being prepared by another group, Insan. Four other defectors from Deraa have made their way to the Jordanian capital, Amman, in recent days and are also briefing investigators.

Defections have been regularly reported during the uprising, but on a small scale. Apart from the apparent mutiny of half a base in the northern town of Jisr al-Shughour (where Syrian officials claim soldiers were massacred by terrorists), none of the defections have been large enough to pose a threat to command and control of the army.

Wasid says his anger is directed not at the government, which he believes betrayed him, but at his army colleagues who stayed behind despite also seeing what he had seen in Deraa. "There were around 100 people each week killed there. They were civilians.

If I see my colleagues again, not only will I tell others what they have done, but I will find their families and tell them too. And then I will hurt them."