At least 17 people were killed in weekend clashes in the Central African Republic's capital, Bangui, the Red Cross says.
The fighting broke out after former rebels patrolling a stronghold of ousted President Francois Bozize came under attack, a spokesman for the new government said.
Rebel leader Michel Djotodia was declared interim president on Saturday.
His Seleka rebel group captured power more than three weeks ago.
The fighting on Saturday and Sunday was the most serious in Bangui since Mr Bozize was overthrown, correspondents say.
A mortar fell on a Baptist church on Sunday, killing three people, residents told BBC Afrique.
The pastor's arm was amputated after he was wounded in the attack, residents added.
Interim government spokesman Gen Moussa Dhaffane said fighting first erupted when youths attacked the former rebel forces in the area of Boy-Rabe, seen as a stronghold of Mr Bozize.
Local Red Cross officials said 17 people were killed in clashes in different parts of Bangui.
The fighting led to some residents fleeing the city, AFP news agency reports.
Residents told BBC Afrique that many youths were frustrated with the insecurity in Bangui.
Some accused Seleka fighters of widespread looting.
The national transitional council, formed after Mr Bozize was ousted, elected Mr Djotodia as interim president on Saturday.
Mr Djotodia was the only candidate in the vote.
A statement signed by "President Francois Bozize's department of communication" and sent to AFP said he "firmly condemns the coup".
"A large part of the Central African territory is left to organised pillaging of its mining resources, including by multinational companies, as the international community looks on complacently," it said.
Mr Bozize fled to Cameroon as the rebels advanced.
Mr Djotodia said he would hold elections within 18 months.
Seleka, an alliance of armed groups, seized power after a peace deal negotiated with Mr Bozize collapsed.
Mr Djotodia is a former civil servant who fell out with Mr Bozize and went into exile, before returning under the peace deal in January as defence minister.
He resigned in March before seizing power.
Correspondents say he does not have widespread international support and has fallen out with some of his former allies.
CAR has an unstable history and is extremely poor, though it has large deposits of minerals including gold and diamonds.