A former prime minister of the Central African Republic held a slim lead in a presidential election many voters hope will end years of violence between Muslims and Christians, initial results showed on Saturday.

With all votes from the capital counted, the National Election Authority said Faustin Archange Touadera, prime minister from 2008 to 2013, had 30,999 votes followed by another former prime minister, Anicet Georges Dologuele, with 28,162.

Mainly Muslim rebels from a group called the Seleka seized power in the majority Christian nation in early 2013, forcing President Francois Bozize to flee and provoking reprisals from Christian anti-balaka militias.

Leaders have since fueled a cycle of religious and inter-communal violence that has killed thousands and forced a fifth of the country's five million people to flee their homes.

Authorities repeatedly delayed Wednesday's election, not least due to violence in the capital Bangui in September, and the new president will face the challenge of disarming militias and convincing their leaders to cede territory.

The Seleka withdrew from Bangui after their leader Michel Djotodia stepped down from the presidency in 2014 and the group's factions have entrenched themselves in the northeast, leaving the country effectively partitioned.

Thirty candidates are competing in the presidential election, which is seen as key for a transition to democracy. All the seats in the National Assembly seats are also being contested.

Bilal Nzanga-Kolingba, son of a former president, was third with 25,055 votes while Jean Serge Bokassa, son of former dictator Jean-Bedel Bokassa had 10,672.

A third former prime minister Martin Ziguele was fifth with 9,946 votes, the electoral authority's spokesman Julius Ngouade Baba told a news conference, adding that the national turnout was 72.2 per cent.

Interim President Catherine Samba-Panza, who has held office since May 2014, is barred from standing.

It was unclear whether Bangui's results represented national sentiment. A second round will be held on January 31 if needed.

The country's economy is struggling, with uranium deposits undeveloped, the cotton sector in trouble and gold and diamond mines under the control of militias.