The alleged killings Thursday in Maiduguri occurred as a human rights group charged the military with widespread abuses in its attempts to subdue the Islamic group, the BBC reported.
An imam (prayer leader), Milam Ajar Mustapha, said he saw 48 bodies in a morgue when he went to collect the remains of four of his sons killed by Nigerian troops.
Mustapha said he and his children were taken by soldiers to an open field after morning prayers Thursday. He said many people were already there and all were told to lie on the ground.
As people were called forward for screening against photos on a computer database, some of them were separated from the group and shot, Mustapha said.
In a report issued the same day, Amnesty International accused the Nigerian military of killing, torturing and burning the houses of innocent civilians.
Responding to the report, Finance Minister Ngozi Okonjo-Iweala said, "All countries, when the security of their citizens is at stake, they try to use all the tools at their disposal."
Boko Haram leaders told journalists Thursday they were ready to sit down for peace talks if the government met their demands, This Day reported.
The group said it wanted peace talks to be held in Saudi Arabia and set out a list of people, headed by the former head of state, Maj. Gen. Muhammadu Buhari, it wanted on the government delegation in the talks.
A spokesman, Abu Mohammed Ibn Abdulazeez, said all Boko Haram members detained by the government must be released, the group compensated and its mosques rebuilt, and wives of Boko Haram members must be welcomed into society.
A spokesman for President Goodluck Jonathan was non-committal about the Boko Haram demands.
"If what the proposed cease-fire is intended to achieve are the objectives of peace and security, then it is a welcome development," Dr. Reuben Abati said.