The stunning announcement came just hours after electoral officials had declared Deby, 68, the winner of the April 11 presidential election, paving the way for him to stay in power for six more years.
Deby "has just breathed his last defending the sovereign nation on the battlefield" over the weekend, army spokesman General Azem Bermandoa Agouna said in a statement read out on state television.
Deby’s campaign said on Monday that he was headed to the frontlines to join troops battling "terrorists".
The circumstances of Deby’s death could not immediately be independently confirmed due to the remote location. It was not known why the president would have visited the area or participated in ongoing clashes with the rebels who opposed his rule.
Rebels based across the northern frontier in Libya attacked a border post on election day and then advanced hundreds of kilometres south across the desert.
Deby came to power in a rebellion in 1990 and is one of Africa’s longest-serving leaders.