Discussing Friday's report, entitled "Erased identity: Muslims in ethnically cleansed areas of the Central African Republic," Joanne Mariner, a senior crisis response adviser at the UK-based organisation, said Muslims in the western half of the country were being repressed and forced to abandon their religion.
More than 30,000 Muslims are living in seven enclaves, guarded by UN troops, across the country, but for those living outside, especially in rural areas, they are being targeted with impunity, the report found.
"They not allowed to express themselves as Muslims; if they are outside the enclaves, they cannot pray, dress in any way that identifies them as Muslim," Mariner said.
"Their survival depends on a daily routine of negotiation with anti-Balaka fighters."
Mariner said that many had been forced convert to Christianity or face persecution from the community
'Failed state'
More than one million people have been displaced since Muslim-led Seleka rebels took control of Bangui, the capital, in March 2013.
Following a spate of abuses by the Seleka rebels, vigilante groups known as anti-Balaka (anti-machete) emerged to fight off the new leadership.
But the anti-Balaka, made up of animist and Christian fighters, also targeted the country's Muslim minority, seen as sympathetic to the Seleka.
Amnesty's report, based on a series of interviews with residents across CAR, says militias "unleashed a violent wave of ethnic cleansing aimed at forcing Muslims to leave the country".
"The continued insecurity and threat from the anti-Balaka comes from there being an absence of a state," Mariner said.
Meanwhile Doctors without Borders (MSF) has previously described the country to be in a state of a protracted chronic health emergency.
CAR has been led by a transitional government since January 2014. The country is scheduled to hold presidential and parliamentary elections on October 18.
Source: Al Jazeera.