The decision was made by judges at the International Criminal Court (ICC) last month just two days before Burundi on October 27 became the first nation to quit the tribunal. But it had been kept under seal until today.
In the decision, the judges authorised ICC chief prosecutor Fatou Bensouda "to open an investigation regarding crimes within the jurisdiction of the court allegedly committed in Burundi or by nationals of Burundi outside Burundi since 26 April 2015 until 26 October 2017."
A violent political crisis was triggered in Burundi when President Pierre Nkurunziza ran for a third term in office, winning July 2015 elections which were boycotted by the opposition.
In a swift reaction, Burundi presidential office spokesman Willy Nyamitwe denounced the "corrupt" ICC in a tweet.
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He accused the court of cheating and said it had just "shot itself in the foot."
"Without any doubt, Burundi will emerge the winner of this battle," he added.
Although Burundi officially left the ICC on October 27, the court said it "retains jurisdiction over any crime within its jurisdiction up to and including 26 October, 2017, regardless of Burundi's withdrawal".
Bensouda opened a preliminary probe in April 2016 into reports of killings, torture and rape amid the political upheavals in the landlocked country in the Great Lakes region.
The judges found there was now "a reasonable basis to proceed with an investigation in relation to crimes against humanity".
The court said according to estimates "at least 1,200 people were allegedly killed, thousands illegally detained, thousands reportedly tortured and hundreds disappeared".
They warned that if "sufficient evidence" is found the prosecutor could "issue either summonses to appear or warrants of arrest".
According to differing tolls provided by the UN or NGOs, the violence in Burundi has claimed between 500 and 2,000 lives, and more than 400,000 Burundians have fled abroad.
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