More than 1,200 Muslims have fled Central African Republic's (CAR's) capital Bangui amid escalating violence.

A convoy carrying the fleeing Muslims headed to two cities in the north of the country, considered relatively safe.

"I leave with a heavy heart, but we have been chased from here," Bangui resident Tonga Djobo told AP.

As soon as the convoy left, rebels looted houses, business and mosques, witnesses said.

"We didn't want the Muslims here and we don't want their mosque here anymore either,'' looter Guy Richard said.

Muslims in CAR are being targeted by Christian anti-balaka militia after violence erupted in the country last December. Thousands have fled Christian-majority areas as sectarian violence continues to rise.

At least 22 people, including 15 local chiefs and three members of staff of the medical charity Medecins Sans Frontieres (MSF), were killed in an attack last Sunday.

The CAR conflict has pitted Muslim Seleka forces against Christian Anti-Balaka militias following the overthrow of former president Francois Bozize, a Christian, by Michel Djotodia, a Muslim.

The two warring factions have engaged in a tit-for-tat violence that has resulted in over 2,000 deaths and hundreds of thousands of displacements since.

Following months of fighting, Djotodia resigned, accused by many of being unable to halt the conflict.

The brutal ethnic cleansing has been strongly condemned by several NGOs.

A UN humanitarian official has warned against the risk of genocide as the conflict "has all the elements that we have seen elsewhere, in places like Rwanda and Bosnia."

Amnesty International has accused peacekeepers of failing to prevent the conflict, while the international war crimes prosecutor has opened an investigation.

Some 4,000 African troops and 2,000 French troops are currently trying to quell the fighting and EU foreign ministers have agreed to send up to 1,000 troops to help end the violence.