Youssouf Tom, Chad Chief Prosecutor, said they were among insurgents arrested during a recent operation against the sect.
He made the disclosure on Chad national television at the weekend.
The group were part of 58 fighters nabbed after the major onslaught at the Lake Chad region.
“Following the fighting around Lake Chad, 58 members of Boko Haram had been taken prisoner and sent to Ndjamena for the purposes of the investigation.
“On Thursday morning, their jailers told us that 44 prisoners had been found dead in their cell,” Tom announced.
The official said he had visited the scene and that investigation was ongoing to determine how they died.
Chadian dealt decisively with Boko Haram to the admiration and ovation of the international community, including Nigerians.
President Idriss Deby ordered the operation after the terror group killed over 90 soldiers in Boma late March.
Chadian soldiers destroyed the sect’s bases, recovered hundreds of weapons and killed over 1,000 members, according to Deby.
AFRICA TODAY NEWS, NEW YORK