"So far we have 54 dead," said the official, who requested anonymity, of the raid on four villages just outside Chibok, where Boko Haram kidnapped more than 200 schoolgirls in April.
The gunmen hurled explosives into churches during Sunday services and fired on worshippers as they tried to flee, witnesses reported.
A local leader in Chibok, who also asked that his name be withheld, said residents had discovered at least 47 bodies in the surrounding bushland, but told AFP the search was ongoing and figures were still being collated.
Federal government spokesman Mike Omeri confirmed Monday that "a number of people were killed" but said he had not yet received an official casualty report from the local government and could not discuss specifics.
Responding to allegations that the military ignored distress calls made after the attack began and left locals defenceless through the insurgent attack, Omeri said: "I was... reliably informed that the military and the airforce were there. Maybe a little late, but they made it there."
But the Chibok leader challenged the government claim, saying the military "did not attempt go" to the scene of the attack.
"Anybody who tells you the military went there is lying," he added.
The targeted villages have been identified as Kwada, Ngurojina, Karagau, Kautikari, all in Borno state, the stronghold of the Islamist group which has killed thousands during a five-year extremist uprising.
The villages are all within 10 kilometres (six miles) of Chibok, where Boko Haram stormed a secondary school on April 14 and abducted 276 teenage girls.
Some escaped within hours of the attack, but 219 remain in captivity.
