An earlier toll had said at least 30 were killed in Tuesday's outbreak of fresh sectarian violence in the country's northwest, with dozens more wounded.
"The latest toll of the clashes in Garga is nearly 50 dead, most of them people who were shot dead in cold blood in their homes," the official told AFP on Wednesday, referring to the small mining town caught up in the violence.
The fighting stopped Wednesday, allowing local Red Cross rescuers and relatives of those killed to bury their dead, said the source, who did not wish to be named.
Most Garga residents have left the town and "many are hiding in the bush," the source said.
Former rebels from the Seleka coalition set up base in the region several months ago, warning operators and others not to go near the mines.
Outraged farmers then created self-defense groups and attacked the group's base on Monday morning, said the official.
The former rebels reacted by "going from home to home searching for men and youths, who they systematically gunned down," after accusing them of working with the self-defense groups.
Witnesses contacted by AFP at Bossembele, about 50 kilometers (30 miles) from Garga, said residents "continue to flee the region on Wednesday with their belongings or empty-handed".
The poor, landlocked nation has been mired in chaos since the Seleka coalition of rebels ousted longtime president Francois Bozize in March.
A new government incorporating Seleka members and led by a former rebel chief, Michel Djotodia, was then put in place. Seleka was disbanded in name but continues to operate as a proto-militia in the region.
Djotodia, who has struggled for months to restore order and to distance himself from the very allies that put him in power, again sought to re-establish authority Wednesday by sacking communications minister Christophe Gazam Betty, the third ex-Seleka minister to lose his post in recent weeks.
The government also Wednesday appointed 12 commanders to head military taskforces of between 200 and 400 men around the country in a bid to improve the security situation.
The forces are a mix of soldiers from Central African Republic's former armed forces (FACA) and Seleka members who were integrated into the army.
As a result of the unrest, some 1.6 million people nationwide -- one third of the population -- need humanitarian aid and nearly 300,000 are internally displaced or have fled to neighboring countries, according to UN figures.
The UN Security Council will vote on a resolution on Thursday that takes the first steps toward sending a peacekeeping force to end anarchy in the Central African Republic, diplomats said.
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