The victims were suspected of being members of a Christian militia that attacked the capital on Thursday, unleashing retaliatory violence across the city.
At a news conference, Djotodia acknowledged the difficulties of controlling the ex-Seleka fighters, who came from several different northern rebel groups with the common goal of ousting President Francois Bozize from power in March after a decade in office.
"There are allegations that I cannot control my men. ... I only know those who are with me," said Djotodia, who has traded his former rebel fatigues for a presidential gray suit and black tie. "Those who aren't how can I control them? I am not God, I hope. I am a man like you. And this country is vast 623,000 square kilometers."
"You could bring an angel from the sky to govern this country and there would still be problems," he added.
Djotodia has formally dissolved the Seleka alliance of rebel groups, and his fighters now consider themselves soldiers in the national army. As hundreds of French troops have arrived, Djotodia has urged his ex-Seleka fighters to get off the streets. On Sunday, the president reiterated that national forces would remain in their barracks.
However, the ex-rebels' spray-painted pickup trucks bounced Sunday over rutted roads around Bangui, particularly in several predominantly Muslim neighborhoods. Half a dozen ex-Seleka fighters sat near Communautaire Hospital in the capital Sunday with a pickup truck full of rocket-propelled grenades.
French Foreign Minister Laurent Fabius said 394 people were killed over just three days, and the local Red Cross said nearly 400 bodies had been collected as of late Saturday.
Dozens of unclaimed corpses lay Sunday under white plastic sheeting in a cement courtyard outside Communautaire Hospital. The buzz of flies was deafening and the stench of death overwhelming to passers-by. Officials expected the death toll to rise further.
"We're sending out five more teams today, as we are still finding bodies several days later," said Jean-Moise Modessi-Waguedo, head of emergency operations for the local Red Cross. He spoke through a mask covering his face.
French forces fanned out across Bangui on Sunday and also had made their way north to the highly volatile town of Bossangoa, where some 40,000 Christians are seeking refuge at a Catholic mission and more than 7,000 Muslims have also fled their homes amid the rising sectarian violence.
In a delicate operation seen as key to restoring durable calm, French troops are going to start Monday trying to disarm fighters, said French defence Minister Jean-Yves Le Drian.
"The period of impunity is over," he said on RTL radio Sunday. "First, we will ask them nicely. If they don't respond, we will force them to."
French President Francois Hollande announced on Saturday that France was raising its Central African Republic deployment to 1,600 troops from about 400. Hollande's office said African Union nations also had agreed to increase their total deployment to 6,000 troops for the Central African nation up from about 2,500 now.
The European Union announced that it's sending in humanitarian aid flights starting Monday to ferry goods and personnel into the country to help the displaced and needy.
In a sign of the tensions, regional peacekeepers stood guard outside Sunday Mass at Paroisse St. Paul along the Ubangui River. The church set up loudspeakers to broadcast the service as an overflow crowd gathered for the service.
As the sermon calling for peace echoed across the lawn outside, women ground manioc with large sticks and sold papaya and dried fish to the hundreds of displaced people camping on the site.
"We are asking Christians to pursue peace and forgiveness, to not seek vengeance or commit reprisal attacks," said Bangui Archbishop Dieudonne Nzapalainga.
One of the world's poorest countries, Central African Republic has been wracked for decades by coups and rebellions. At the time of the March coup by Seleka, religious ideology played little role in the power grab.
Seleka are blamed for scores of atrocities since taking power, even tying civilians together and throwing them off bridges to drown and burning entire villages to the ground. Anger over such abuses has fanned a backlash against Muslim civilians, who make up only about 15 per cent of the population.
-AP
