Syria is holding tens of thousands of detainees in a "torture archipelago", a US-based rights group said on Tuesday, after the UN rights chief accused both government and opposition of "serious" violations.

As Turkey reported a new mass defection of Syrian troops across the tense border, Syrian President Bashar al-Assad said he regretted that his country's defence forces shot down a Turkish fighter jet on June 22, but still insisted the plane was in Syrian airspace.

Rights monitors, meanwhile, reported 78 confirmed dead in violence on Monday as exiled opposition groups gathered for a second day of talks to try to forge a common vision for a transition in Syria from Assad's rule.

The New York-based Human Rights Watch documented 27 detention facilities across Syria it said were used to hold people swept up in the government's crackdown on an uprising now in its 16th month.

The group said it had carried out more than 200 interviews with former detainees, and military and intelligence defectors, "almost all" of whom described experiencing or witnessing torture, including "prolonged beatings, often with objects such as batons and wires."

Other methods included "holding the detainees in painful stress positions for prolonged periods of time, often with the use of specially devised equipment, the use of electricity, burning with car battery acid, sexual assault and humiliation, the pulling of fingernails, and mock execution."

Human Rights Watch said that in addition to the 27 facilities -- operated by four main intelligence agencies commonly referred to as the "mukhabarat" -- detainees were being held in stadiums, military bases, schools and hospitals.

A 31-year-old detainee held in Idlib province in the northwest was quoted as saying that interrogators had squeezed his fingers with pliers and put staples in his fingers, chest and ears.

"I thought I would never see my family again. They tortured me like this three times over three days."

The report quoted a former intelligence officer as describing a wide range of torture methods, including hanging prisoners by their hands from the ceiling and putting prisoners in coffins and threatening to kill them.

In New York, UN High Commissioner for Human Rights Navi Pillay said that government and opposition alike were carrying out "serious" new rights violations including attacks on hospitals.

She told the UN Security Council that the violence was becoming "increasingly sectarian," while hundreds of people remain trapped in Deir Ezzor, in the east, and in the Old City district of Homs "because of the increasing use of heavy weaponry, shelling and ongoing armed clashes."

With the United Nations considering the future of its observers in Syria, Pillay said she told the council it must "support and strengthen" the UN Supervision Mission in Syria so that it can "effectively" monitor events.

She told reporters after the briefing that the violence was being fuelled by arms supplies from abroad to both the government and the opposition.

"Any further militarisation of the conflict must be avoided at all costs," she said.

While Pillay did not name countries, Russia and Iran are key suppliers to Assad's government, while Gulf states, notably Qatar and Saudi Arabia, have given weapons to the increasingly well-armed opposition.

The core of the rebel Free Syrian Army is made up of defectors from the regular armed forces who have been breaking ranks in growing numbers in recent months.

A total of 85 defecting soldiers, including a general, crossed the border into Turkey on Monday, the Anatolia news agency reported.

Tensions on the border have soared since Syria shot down a Turkish F-4 Phantom jet last month.

Assad said in an interview published by Turkey's Cumhuriyet newspaper on Tuesday that he regretted the incident "100 percent".

But he rejected Turkey's accusations that the Syrian defence forces intentionally shot down the aircraft, which was on a training mission over the Mediterranean.

"A country at war always acts like this, this plane was flying at a very low altitude and was shot down by anti-aircraft defences which mistook it for an Israeli plane, which attacked Syria in 2007."

He sent his condolences to the families of the two pilots of the downed plane, who have not been found.

The rebel Free Syrian Army is boycotting a meeting of opposition groups in Cairo, which entered its second day on Tuesday, saying that foreign military intervention and arming its fighters should be on the agenda.

Arab League chief Nabil al-Arabi, who was chairing the talks attended by around 250 opposition figures, urged the factions "not to waste this opportunity" and to "unite."

On the ground, 44 civilians were among 78 people confirmed killed on Monday, the Syrian Observatory for Human Rights said, putting the overall toll since the start of the uprising at more than 16,500.