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He was reported dead on Tuesday, a day after he won re-election for a sixth term in office.
The Chadian national army confirmed his death from gunshot injuries in a fight with rebels.
The president was commanding his army in the battle against rebel forces in the far north over the weekend.
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There has been a prolonged battle in the African country between government forces and the rebel Front for Change and Concord in Chad (FACT).
The unrest had escalated in recent days as anti-government fighters approached N’Djamena, the capital city.
Azem Agouna, a spokesman of the Chadian army, said in a broadcast that the late leader “breathed his last defending the sovereign nation on the battlefield”.