The Bishop of Yola told the BBC the insurgents had locked the church and "cut people's throats" in Waga Chakawa village, Adamawa state.
On the same day, militants also attacked Kawuri village in neighbouring Borno state, killing 52 people.
Both assaults were blamed on the Islamist Boko Haram group.
The organisation - whose name means "Western education is forbidden" - is especially active in the north-east of the country.
Boko Haram wants to impose a severe form of Islamic law, and has been blamed for thousands of deaths.
Borno and Adamawa are two of three north-eastern states - along with Yobe - put under emergency rule last May, as the military attempts to combat the insurgency.
The Bishop of Yola, Mamza Dami Stephen, said parishioners had told him about what happened on Sunday morning.
They described how the insurgents had arrived on trucks and locked the church "towards the end of the service".
"Some people tried to escape through the windows and the [attackers] shot at them," the bishop said.
What is Nigeria's Boko Haram?
The militants set off bombs, before burning houses and taking residents hostage during a four-hour siege.
The bishop said locals were gripped by terror.
"Everybody is living in fear," he explained.
"There is no protection. We cannot predict where and when they are going to attack. People can't sleep with their eyes closed."
In neighbouring Borno, gunmen targeted a busy Sunday market in Kawuri village. After setting off bombs, they killed civilians in their homes and set ablaze dozens of houses.
Earlier this month, Nigerian President Goodluck Jonathan sacked his military high command.
No reason was given, but the move came amid concern that Boko Haram have been able to continue their bloody campaign despite the wide-ranging powers given to the military to tackle the insurgency last year.
Since the state of emergency was imposed in May, UN figures suggest more than 1,200 people have been killed in Islamist-related violence.
A senior cleric has spoken of how suspected Islamist militants "slaughtered" some 30 churchgoers in north-eastern Nigeria on Sunday.