Gunmen stormed Sunday services in four villages near Chibok in Borno state where Boko Haram kidnapped more than 200 schoolgirls on April 14.
They hurled explosives into churches, torched buildings and fired on worshippers as they tried to flee, residents said.
"So far we have 54 dead," said a Borno state official, who requested anonymity as he was not authorized to discuss casualties with the media.
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 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.
Locals have accused the military of ignoring distress calls made after the attack began, leaving them defenseless during the attack, but Omeri said: "I was... reliably informed that the military and the airforce were there. Maybe a little late, but they made it there."
The Chibok leader challenged the government's version of events, saying the military "did not attempt go" to the scene of the attack.
"Anybody who tells you the military went there is lying," he said.
In the week following the April abductions, Chibok residents accused the security forces of doing almost nothing to secure the girls' release, despite military claims that a massive manhunt had been launched.
The United States, Britain, France and Israel are now supporting Nigeria's search-and-rescue operation, but there have been no signs of success so far, with 219 girls still missing.
The villages targeted on Sunday -- Kwada, Ngurojina, Karagau and Kautikari -- are all within 10 kilometers (six miles) of Chibok.
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