They say they found the bodies in Damasak in north-eastern Nigeria, a town they entered on Saturday, ending months of Boko Haram control.
Nigeria's President Goodluck Jonathan predicted all territory would be taken back from Boko Haram within a month.
"They are getting weaker and weaker by the day," he told the BBC on Friday.
The victims, many with their throats slits and some decapitated, may have been killed some time ago, reports suggest.
Chadian army Col Azem Bermandoa Agouna told AFP news agency that he had visited the grave and seen "about 100 bodies spread under a bridge just outside the town".
Together with the Nigerian army, forces from Chad, Niger and Cameroon are involved in an offensive against the Islamic militants who are controlling parts of north-eastern Nigeria.
Nigeria is preparing to hold presidential elections on 28 March after security concerns led to a postponement of the original date in mid-February.
Source - BBC
Image Credit - REUTERS