Prosecutors had earlier said that Maxime Mokom, a former national coordinator of so-called anti-balaka militias, played a key role in a plan to violently target the Muslim civilian population in 2013 and 2014.
"Having considered the totality of the evidence in the Mokom case and in light of changed circumstances regarding the availability of witnesses, there are no longer any reasonable prospects of conviction at trial even if the charges were confirmed," the prosecutor's office said.
At a hearing in August, Mokom said he had played no part in any of the violent attacks on Muslim civilians in 2013 and 2014 that prosecutors wanted to charge him with.
He told the court he was a refugee stuck in the neighbouring Democratic Republic of Congo for most of the period referenced in the charges, while the prosecutors said he coordinated the deployment of militias and oversaw attacks.
CAR has been mired in violence since a coalition of mostly northern and predominantly Muslim rebels known as Seleka, or "Alliance" in the Sango language, seized power in March 2013.
Their dominance gave rise to the opposing anti-balaka Christian militias.The ICC has been investigating the violence in CAR since May 2014. There are two ongoing trials before the court involving two other anti-balaka leaders and one Seleka leader.
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