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Boko Haram has stepped up assaults in recent weeks across the region in what appears to be a fight back against an offensive mounted by soldiers from Nigeria and its neighbors, Chad, Cameroon and Niger.
"The two villages were attacked by surprise on Saturday and Sunday night. There were 13 dead in each attack," said a Chadian official who declined to be named.
Merom village was attacked on Saturday by armed men who slit the throats of their victims and burned houses before fleeing, the source said. Other local officials gave similar accounts.
Militants also attacked a group of camel herders at the village of Tiskra, cutting 13 people's throats before fleeing when guards of the village chief opened fire, the source said.
Boko Haram, fighting to carve out an Islamist state in northeast Nigeria, has also launched a string of cross border raids.
Last week, more than 200 people died in a string of attacks inside Nigeria, piling pressure on new President Muhammadu Buhari.