Three ex-rebels shot dead by French troops in the capital of the Central African Republic on Sunday were members of the presidential guard and were "killed in cold blood", the CAR presidency said.

"They were killed in cold blood by members of Sangaris," presidential spokesman Guy Simplice Kodegue said on Monday, referring to the French force sent this month to disarm ex-rebels sowing chaos in the country.

They are "members of the presidential guard," he told AFP.

President Michel Djotodia, who became the first Muslim leader of the majority Christian nation after a March coup, was formerly leader of the Seleka rebel coalition.

He has officially disbanded Seleka but some members went rogue, leading to months of killing, raping and pillaging -- and prompting Christians to form vigilante groups in response.

The French army said its troops opened fire in Bangui on Sunday against "a group of half-a-dozen people suspected of being ex-Seleka" and who "were preparing to use their weapons".

But the presidential spokesman said the shooting was unprovoked.

"This was not a disarmament operation and no shots were fired, contrary to what was reported in certain French media," Kodegue added.

He said the ex-rebels were driving in a vehicle when they were stopped.

"They were shot dead despite having shown their badges and papers proving their mandate."

"It was deliberate," he charged.

France has deployed 1,600 soldiers to its former colony alongside the African Union's UN-mandated MISCA force to try to quell rising sectarian violence.

The French intervention has been largely welcomed by the Christian majority but many Muslims argue operations against the remnants of Seleka have left them exposed to reprisals.

On Sunday several thousand Muslims protested in Bangui against French troops, as reports emerged they had shot three ex-rebels.

Amnesty International says an estimated 1,000 people have been killed since December 5, mostly by Muslim ex-rebels but also in Christian reprisals.