Earlier estimates put the number of fatalities at about 40.
"The latest toll from the violence established by hospital sources is 61 dead and 300 hurt," said a statement from the minister of public safety, Dominique Said Panguindji.
The violence began on September 26 after the murder of a Muslim driver and then spread to several districts of the city before French troops and UN peacekeepers restored calm.
Protestors threw up roadblocks and demanded the resignation of country's interim president, Catherine Samba Panza, who was attending the UN General Assembly in New York. More than 30,000 people were forced from their homes.
In remarks broadcast on national radio on October 1, she denounced "an orchestrated manipulation by part of the population" to incite people "to rise up and resurrect sectarian conflicts".
The country was shaken in late 2013 by months-long violence between Christians and Muslims, triggered by the ousting of the then president Francois Bozize, a Christian, by mainly Muslim Seleka rebels.
UN rights investigators said earlier this year that estimates of between 3,000 and 6,000 dead in that bout of fighting failed to capture "the full magnitude of the killing".
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