The bodies, which were partially mummified by the dry desert air, were reportedly scattered beneath a bridge on one of the main roads leading out of the town. Many had their throats slit and some had been decapitated. The victims have yet to be identified.
Chad's military spokesman Colonel Azem Bermandoa Agouna was quoted as saying that "there are about 100 bodies spread around under the bridge just outside the town… this is the work of Boko Haram."
The horrendous discovery came a day after Nigeria's President Goodluck Jonathan told the BBC that all the territory in his country's north that has been seized by Boko Haram can be "retaken in a month".
Apart from Nigeria, troops from Chad, Cameroon and Niger are taking part in an offensive against Boko Haram militants who started to seize territory about a year ago.
Earlier in March, Boko Haram pledged allegiance to the Islamic State, which has captured large areas in Syria and Iraq in the past year.
More than 15,000 people have already been killed as a result of Boko Haram attacks in north-eastern Nigeria as of 2012.