Some 40 buses and ambulances move civilians to Idlib province as evacuees bid emotional goodbye to war-torn city.

At least 3,000 civilians were evacuated from east Aleppo under a deal allowing Syria’s regime to take full control of the city after years of fighting, the International Committee of the Red Cross (ICRC) said.

A revived agreement on a ceasefire and the evacuations were announced on Thursday after an initial plan for civilians and fighters to leave rebel-held parts of the city collapsed the previous day amid renewed clashes.

Despite the evacuation, the United Nations warned almost 50,000 remained in the war-torn Syrian city.

The evacuation began with a convoy of ambulances and buses crossing into a government-held district in southern Aleppo at 2:30pm local time (12:30GMT). A slow-moving convoy of two dozen vehicles snaked out of al-Amiriyah district and crossed into government-held Ramussa en route to rebel-held territory in the west of Aleppo province.

This is what the start of evacuations looked like in East Aleppo. @ZouhirAlShimale was there when ambulances were loading the injured. pic.twitter.com/z6mb07qGO4 — Al Jazeera English (@AJEnglish) December 15, 2016

Earlier, the evacuees spent hours gathering at a staging area in al-Amiriyah. An AFP news agency correspondent saw people piling on to the green buses, filling seats and even sitting on the floor, with some worried there would not be another chance to flee.

Many were in tears and some hesitated to board, afraid they would end up in the hands of regime forces.

On the dusty window of one of the buses someone had written “One day we will return”.

Each bus carried a member of the Syrian Red Crescent wearing the organisation’s red uniform, riding at the front next to the driver.

As darkness fell over the city, a third convoy was in the process of evacuating more citizens, Syrian state television reported.

But the evacuation got off to a shaky start on Thursday.

Ibrahim Abu Allaith, of the Syrian Civil Defence, told Al Jazeera that militias loyal to Syrian President Bashar al-Assad reportedly killed at least one person and injured four more while firing on the first convoy of wounded evacuees.

AFP reported that the first convoy was led by vehicles from ICRC and the Syrian Arab Red Crescent, followed by ambulances and then the green buses.

The head of the ICRC in Syria, Marianne Gasser, said it could take days to complete the evacuation.

“Right up until the last minute, it wasn’t clear we’d get into east Aleppo,” Gasser said in a statement.

“A crane was used to remove some of the debris from the street so the ambulances and buses could get through. There were burned cars. Smoke rising from nearby buildings. There was a lot of fear and uncertainty.

“When we arrived, the scene was heart-breaking. People are faced with impossible choices. You see their eyes filled with sadness,” she said.

UN envoy for Syria Staffan de Mistura said about 10,000 people, including fighters, were likely to be evacuated to the rebel-stronghold of Idlib.

“There are about 50,000 people, including 40,000 civilians, that will go to west Aleppo,” de Mistura said, adding that the remaining 10,000 were made up of between 1,500 to 5,000 fighters and their families.

Zouhir Al Shimale, an independent journalist in east Aleppo, said the evacuation went ahead despite the attacks on the first convoy.

“There hasn’t been fighting since the morning,” he told Al Jazeera, explaining “hundreds of families” have gathered at the departure point for the buses.

“Civilians are given the choice to stay or leave. If they stay, they’ll be under regime control. Most of the people want to go because they are afraid of potential massacres by the regime,” Shimale added.

“In recent days, people are desperate to get to somewhere where we have the supplies – food, medicine, fuel – like we used to have in the days before the siege. Even if they are in refugee camps, but people still want to leave the besieged area.”

IN PICTURES: Ghosts of Aleppo

Meanwhile, Turkish President Recep Tayyip Erdogan said that he discussed the situation in Aleppo “several times” with his Russian and US counterparts, Vladimir Putin and Barack Obama.

He said that he also spoke to German Chancellor Angela Merkel by phone to discuss how Berlin could provide assistance to people in the northern Syrian city.

‘Damascus next’

Marwan Kabalan, a Syria analyst and associate political analyst at the Doha Institute, said he expects the Syrian government to focus its attacks near the capital.

“I think the regime will turn next to targeting the Damascus suburbs,” he told Al Jazeera. “Idlib is becoming a point of exile for fighters … I think it will remain like this till the very end [of the conflict].”

Throughout four years of fighting, Aleppo has seen intense battles that left much of the city in ruins.

Aleppo, a cultural and economic hub second only to Damascus in importance, had been split between a rebel-controlled east and government-held west since 2012.

Syria’s conflict has evolved from largely unarmed protests against Assad into a full-scale civil war that has killed hundreds of thousands and displaced more than half of the country’s prewar population.

Medical workers evacuate an injured man from eastern Aleppo on Thursday December 15 [Malek al-Shimale/Al Jazeera]