The public security ministry did not say who was involved in the fighting or how long it went on, but the area regularly sees clashes between sedentary farmers and nomadic breeders, or other groups, over land.
The latest violence led to 175 people being arrested at the scene, where "a large part" of the village of Tileguey in Ouaddai province was "set on fire by armed men," the ministry said in a statement.
"This deadly conflict has so far left 42 dead," the ministry said on its website.
Chadian media reports said the fighting lasted several days, with some saying it began on Sunday. But the reports could not be verified with the authorities.
"The situation is under control but I'm trying to reconcile the different parties," Public Security Minister General Mahamat Charfadine Margui told AFP in a telephone message.
The minister said he was at the site, around 700 kilometers (435 miles) east of the capital, N'Djamena.
He was heading a government and army delegation, aimed at "shedding full light" on the incident.
Ancestral disputes
In eastern and southern Chad, where many residents are armed, clashes frequently break out as farmers accuse herders of allowing animals to graze on their land or trample on crops.
Most clashes between herders and farmers occur in the annual transhumance corridors where vegetation is thick and suitable for crops and feeding livestock.
However, in Ouaddai, they tend to generally be about land ownership, with villages and clans sometimes killing each other for plots of land.
Such ancestral disputes have grown in recent years in this region of the continent, affecting Sudan, South Sudan, Central African Republic, Cameroon and Nigeria as well as Chad, whose southern or northern parts border the Sahelian strip.
Herders generally come from the arid Sahelian regions and seek to settle on more fertile land where they can raise their camels and sheep.
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