Lt. Gen. Abulaziz al-Shalal is one of the highest-ranking officials to join the uprising against the Syrian regime.
The army had failed to protect Syrians and turned into “gangs of murder”, the general said in a video statement.
The announcement came amid reports of a deadly government strike in the northern province of Raqqa.
After reportedly crossing the border into Turkey, Gen. Abulaziz al-Shalal released a statement saying he had defected because the military had perpetrated massacres in towns and villages instead of protecting Syrians.
“I declare my defection from the army because of its deviation from its fundamental mission to protect the nation and transformation into gangs of murder and destruction,” he said in a video message posted online.
Opposition sources said the commander had been secretly co-operating with the rebels from the outset.
This is believed to be the case with many other senior defectors, our correspondent adds.
But Gen. Abulaziz al-Shalal said defecting was becoming more difficult because of the increased level of surveillance.
“Definitely, there are other high-ranking officers who want to defect but the situation is not suitable for them to declare defection,” he said.
An unnamed Syrian security source confirmed the army chief’s defection but played down its significance, Reuters news agency reports.
Gen. Abulaziz al-Shalal was due to retire soon and joined the uprising to “play hero”, the source is quoted as saying.
Meanwhile, reports of a deadly government strike near a village in the northern province of Raqqa have emerged.
Around 20 people, including eight children, were killed in the shelling, according to the UK-based activist group, the Syrian Observatory for Human Rights.
The organization released video footage purportedly of the victims, showing blood-stained bodies laid out on blankets.
The SOHR is one of the most prominent organizations documenting and reporting incidents and casualties in the Syrian conflict. The group says its reports are impartial, though its information cannot be independently verified
Earlier this week, opposition activists said dozens of people had been killed in a government air strike in the rebel-held town of Halfaya in Hama province.
Although rebels have claimed some major territorial gains in recent months, the regime has hit back with massive firepower at the areas it has lost.
In a separate development, rebel fighters said they had seized the north-western town of Harem near the Turkish border.
On Tuesday the UN peace envoy for Syria Lakhdar Brahimi held talks in Damascus with opposition figures who are tolerated by the regime but not supported by the mainstream opposition, our correspondent says.
Earlier, Lakhdar Brahimi had also met President Bashar al-Assad to discuss “the many steps to be taken in the future” to help end the conflict.
He did not, however, elaborate on what these steps were.
With the government dismissing the uprising as a foreign-backed extremist plot, and the rebels demanding that President Bashar al-Assad leave power immediately, the chances for a peaceful compromise seem slight.
Rebels have been fighting Bashar al-Assad’s government for 21 months. Opposition groups say more than 44,000 people have been killed.
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