He did not say what had happened to Abubakar Shekau, but said he had been replaced by Mahamat Daoud – who has not been heard of before.
Mr Shekau has not featured in the group’s recent videos, leading to speculation that he has been killed.
Mr Deby, whose troops have been involved in battling Boko Haram, said Mr Daoud was open to dialogue.
The BBC’s Nigeria correspondent Will Ross says that last year, the Chadian leader was said to be brokering peace talks with Boko Haram.
But the negotiations never happened and were widely seen as a sham so some analysts will question how much credence to give to Mr Deby’s latest comments about the jihadist group, he adds.