Heavy fighting between Syrian rebels and troops sent thousands fleeing into Turkey on Friday, as President Bashar al-Assad said only the ballot box could decide his future and the main opposition bloc elected a new leader.

The clashes over a border post near the northeastern town of Ras al-Ain killed 46 combatants in two days, a watchdog said, highlighting the humanitarian crisis and regional dangers posed by Syria's nearly 20-month conflict.

On the political front, the opposition Syrian National Council (SNC) meeting in Qatar elected veteran dissident George Sabra, a Christian, as its chief amid US concerns it was unrepresentative of all opposition groupings.

The UN said more than 11,000 Syrians had fled into neighbouring countries in 24 hours, including 9,000 into Turkey, bringing to more than 408,000 the number of registered Syrian refugees in the region.

It said the total number of refugees in Turkey, Lebanon, Jordan and Iraq would likely hit 700,000, and the head of its humanitarian efforts said those in need of emergency aid in Syria would rise to more than four million early next year.

"This will just continue to grow in the terms of humanitarian suffering," said John Ging, who heads the UN's Office for the Coordination of Humanitarian Affairs.

The United States, meanwhile, unveiled another $34 million in aid for refugees, pushing its total donations to Syria to more than $165 million.

At least 20 soldiers were killed in Friday's clashes over the Ras al-Ain post, one of only two crossings on the Turkish border still in regime hands, the Syrian Observatory for Human Rights said.

It said rebels had captured many soldiers and taken control of key positions in mainly Kurdish Ras al-Ain, including the offices of the security and intelligence services.

In an interview with Russian television, meanwhile, Assad said whether he can "stay or leave" was a "popular issue" that can only be decided "through the ballot boxes."

Assad warned Syria was facing a protracted conflict because foreign powers were backing the rebels.

He admitted divisions existed in Syria, but said "division does not mean civil war," and denied his forces had committed war crimes.

State-backed Russia Today had on Thursday released excerpts of the interview in which Assad vowed to "live in Syria and die in Syria" and warned foreign intervention would have global consequences.

A car bomb outside a mayor's office in the town of Muadamiya al-Sham south of Damascus killed four civilians on Friday, the Observatory said, while at least 12 civilians were killed in shelling of the eastern province of Deir Ezzor.

On Friday, at least 114 people were killed nationwide, including 53 soldiers and 47 civilians, it said.

Thousands of protesters rallied on Friday, many mocking Assad's "live and die" remarks.

"Bashar, you will die in Syria, but you won't be buried in the ground, you will be thrown in the dustbin of history!" read one placard in the central city of Hama.

Assad's foes met in Qatar, meanwhile, amid Western- and Arab League-backed efforts for them to unite in a government-in-waiting representing the spectrum of regime opponents.

Before the election of Sabra, a 65-year-old former communist, as new SNC chief, divisions were exposed between the disparate formations.

The SNC had asked for a delay to a decision on uniting Assad's foes until it elected a new leader, but a major activist network, the Local Coordination Committees, quit the bloc and other groups then went on to meet without the SNC.

Earlier, participants said most delegates had agreed on a unified opposition structure that would allow coordinated military action, as well as humanitarian aid and the administration of zones under rebel control.

But representatives of the SNC voiced reservations over the proposal tabled by prominent dissident Riad Seif with apparent US support.

Asked by reporters what he wanted from the international community, Sabra replied: "We have only one demand, and that is to stop the bloodbath and help the Syrian people chase out this bloody regime by providing us with weapons. We want arms."

On the ground, the rebel Free Syrian Army said it was reorganising and relocating its leadership to rebel-held territory.

General Mustafa Sheikh, who heads the FSA military council, told AFP in northern Syria that the group had started to restructure itself into five divisions -- north, south, east and west, and the coast -- and would elect new leaders.

"We are getting closer and closer to becoming organised, so that we can get to a stage that is accepted by the international community," he said.

Sheikh said the FSA leadership, based largely in Turkey, is countering criticism from its rank and file by relocating around 200 officers -- including himself -- to "liberated" parts of Syria.

The Observatory says more than 37,000 people have died since the uprising against Assad erupted in March 2011, first as a protest movement and then an armed rebellion.