A bomb dropped by a Syrian air force jet killed and wounded scores of Palestinians on Sunday in the largest refugee camp in Damascus, sending thousands of residents fleeing for other areas of the capital now besieged by civil war.

The exodus has sparked fears that the flood of refugees into neighbouring countries, which is already straining resources in Lebanon, Jordan and Turkey, will further intensify, with Syria's Palestinian population of 500,000 increasingly caught in the middle of bitter and protracted fighting.

Yarmouk camp, where the attack took place, has steadily been drawn into the conflict in Damascus over the past month. Previously, it had been a relative safe haven as security decayed elsewhere in the capital, which has been assaulted since late November by rebel groups attempting to penetrate the regime's inner defences.

The attack is believed to be the first strike on Yarmouk by an air force jet, the most potent weapon used so far by the regime in its defence of the capital. A bomb dropped from a jet hit a mosque near the centre of the camp.

The death toll is unknown, but videos posted online showed carnage near the mosque and dead and injured people being collected by residents. There were reports that hundreds of families were making plans to flee.

A mass movement of Syria's Palestinian population is considered a nightmare scenario by international humanitarian leaders. Senior figures from the United Nations and the European Union are in the region trying to find ways to manage what they fear could be the next phase of a gathering refugee crisis that has already seen more than 500,000 Syrians flee for neighbouring borders.

Between 1.2 million to 2 million Syrians are also believed to be internally displaced, many facing desperate shortages of food, water, heating and shelter as winter sets in.

"The Palestinians have been on the move for some time now," said the EU's humanitarian aid commissioner, Kristalina Georgieva. "Their situation is especially sensitive because they do not have too many places to go.

"We are looking at finding urgent solutions for them. There is limited capacity in the camps in Lebanon and it is an extremely sensitive issue in Jordanian society to take in extra Palestinians."

So far, only about 500 Palestinians from Syria are registered in Jordan. Another 12,000 are believed to have made it to Lebanon, where 12 refugee camps hold a local Palestinian community of about 280,000 people.

Palestinians in Syria had enjoyed the protection of the Syrian regime for much of the past 40 years. However, their loyalties have been tested as the civil war has intensified. The large majority of the Palestinian population in Syria is Sunni, as is the opposition movement which is attempting to oust the regime of Bashar al-Assad, whose Alawite sect is aligned to Shia Islam.

About half of Syria's Palestinian refugees are thought to remain supportive of the regime; the resthave grown hostile to it as the 21 month crisis has intensified.

Sunday's attack is believed to have occurred after sporadic fighting inside the camp over the past fortnight between rebel units and Palestinian factions loyal to Assad, headed by Ahmed Jibril, a veteran local leader of the Popular Front for the Liberation Of Palestine – General Command.

"They are increasingly being asked to take sides," said Georgieva. "This is a very difficult situation for the Palestinian community and we will do everything we can do make sure that they do not become yet another victim of the terrible events in Syria. One option we will look at is trying to establish safe havens inside the country."

The recognition by more than 100 states of the new Syrian National Coalition as a legitimate representative of Syrian people has made it easier for global humanitarian bodies to begin operating in Syria, where many communities face chronic shortages of food.

Until now, deeply unstable supply lines made it almost impossible to get meaningful supplies into ravaged cities, such as Aleppo in the north and Homs in the west. Aid groups are now trying to establish aid hubs near the Turkish and Jordanian borders and exploring ways to secure routes to battle zones, which will probably require negotiations with rebel groups.

• This article was amended on 17 December 2012. The full name of the organisation of which Ahmed Jibril is a leader was cut short in the editing process. He is part of the Popular Front for the Liberation Of Palestine – General Command, not the Popular Front for the Liberation Of Palestine. This has been corrected.