Expressing regret for the deaths, it put the blame on rebels it said its soldiers had been pursuing and suggested Chad and the CAR -- "two brotherly peoples" -- hold a joint investigation.
Chad's President Idriss Deby, who ruled his country for more than 30 years and was an important Western ally in the fight against Islamist militants in Africa, has been killed on the frontline against rebels in the north.
Deby's son, Mahamat Kaka, was named interim president by a transitional council of military officers.