Malam Aji Mustapha, a religious leader from Maiduguri, told the BBC that 11 young men, including some of his children, were killed allegedly by members of the Nigerian military.
The imam said authorities were rounding up young men based on photo evidence from a computer database.
A report Thursday published by Amnesty International said security forces in Nigeria were "out of control."
"People are living in a climate of fear and insecurity, vulnerable to attack from Boko Haram and facing human rights violations at the hands of the very state security forces which should be protecting them," Amnesty International Secretary-General Salil Shetty said in a statement.
Maiduguri is considered a stronghold of Boko Haram, a rebel group fighting to establish an Islamic state in a country divided along Muslim and Christian lines.
Nigerian Finance Minister Ngozi Okonjo-Iweala told the BBC that security forces were putting their lives at risk in their fight against the militant group. Forces there are trying to prevent "terrorist" attacks, the minister said.
"I think you need to look at the circumstances," she said.