Dozens of civilians have been killed and thousands displaced in the latest attacks, the rights group said in a new report, adding that a range of armed militias "continue to enjoy impunity" because international forces are stretched so thin.
In one attack near Bambari on October 8, the mostly Christian anti-balaka militia stopped a vehicle containing 24 people.
"They let all of the Christians go," a survivor told Amnesty. "All of the Muslim men whom they caught were killed. They undressed their bodies to humiliate them, and cut them into pieces, chopping off their hands and feet."
Many towns and villages have been left nearly deserted by the violence, with around 410,000 people internally displaced over the past 18 months -- many forced into squalid camps or living rough in the bush.
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In the town of Dekoa, Amnesty found the entire Christian population had taken refuge in a church or fled.
On October 10, the mostly Muslim Seleka forces surrounded the church and opened fire with grenades and rifles on the refugees inside. Nine people were killed, including four children.
The rest were saved by the intervention of the French troops.
The town's Muslims were also under threat from other militias. Only 63 Muslims remained from a population of over 1,000, also protected by the small French contingent.
"We're complete prisoners," the town's imam told Amnesty. "We stay close together and hardly move."
French, European and United Nations peacekeepers have saved many lives, Amnesty said, but with the UN peacekeeping force "still several thousand troops short of its mandated numbers, they have not been able to prevent escalating violence in the country's central region."