Arsene Sende told national radio he had instructed prosecutors to open an investigation "because crimes and other grave human rights violations were committed and continue to be committed by ex-president Francois Bozize and some of his allies."
Bozize, 66, was ousted on March 24 by the Seleka rebel coalition in the latest coup in the chronically unstable impoverished former French colony.
Sende alluded to "assassinations, illegal and arbitrary detentions, torture, destruction of homes, kidnappings, summary and extra judicial executions, inciting hatred and genocide, economic crimes and acts compromising civil peace."
He also accused Bozize of being behind the 2010 disappearance of former minister and leader of the Convention of Patriots for Justice and Peace (CPJP) rebel group, Colonel Charles Massi.
"He was arrested in the beginning of 2010 in Chad and handed to Central African authorities, then executed by Bozize's security detail," he said.
Sende said about a dozen Seleka rebels or allies of its leaders were executed on the eve of the coup by an officer in Bozize's presidential guard.
He said the probe would also look into the fate of numerous political prisoners in the Bossembele military camp 150 kilometres northeast of Bangui, allegedly locked up on Bozize's orders.
The deposed leader has sought refuge in Cameroon.
An interim government with coup leader Michel Djotodia as president has vowed to hold free and fair polls at the end of an 18-month transition period.
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