Men and boys were targeted by gunmen after they stormed Njaba in eastern Nigeria before burning the remote village to the ground.
The assault took place early on Tuesday as many villagers in the isolated community were heading to morning prayers.
“The attack was not immediately known because the village is very remote and our men couldn’t access the area,” said a military source.
One woman, Falmata Bisika, 62, lost four of her grandchildren in the raid, which she said was carried out by gunmen “armed to the teeth” with weapons and explosives.
The militants destroyed homes and businesses with petrol bombs and shot anyone attempting to flee, “especially teenagers and the elderly,” she said.
Muminu Haruna, 42, said he hid in a grain silo behind his house for several hours with about eight other people until the gunmen left.
“I participated in the counting of dead bodies… 68 people were killed,” he said in an account supported by two civilian vigilantes.
“These included both males and females, some were slaughtered and others shot dead and most of the houses in our village have been destroyed.”
Another witness, Aminatu Mommodu, said the bodies of victims, including many men with their throats slit, were in the mosque.
Other villagers caught by the gunmen outside the mosque had been shot, she said.
Ibrahim Wagu, a Maiduguri resident who comes from Njaba, told Reuters news agency that two of his relatives had been killed.
“My older brother and my sister’s first son were killed,” he said.
Boko Haram controls large areas of Borno state but in recent months has also carried out cross-border raids into Chad, Cameroon and Niger.
The three countries have joined Nigeria to form a military coalition, which has recaptured several towns and villages in recent weeks.
Chadian forces have recently helped the Nigerian army recapture several towns and villages from Boko Haram.
Njaba is 20 kilometres from the town of Damboa, which was seized by Boko Haram last June, forcing thousands to flee, but later recaptured by troops helped by civilian vigilantes.