The rebels shot dead their victims after looting homes and shops and setting fire to buildings, said Debiro Hawul resident Umaru Markus.
Two teenage girls blew themselves up near a crowded mosque in Maiduguri, killing 30. This is the fourth suicide attack in June by Boko Haram.
Boko Haram took control of a large swath of northeast Nigeria until a multinational force this year forced them out of towns and villages.
Boko Haram last year held a vast swathe of territory in northeastern Nigeria of just over 30,000 square kilometers
Chad, a military heavyweight in the region, has been a driving force behind a campaign that has inflicted a series of defeats on Boko Haram since January.
Boko Haram killed more than 150 people since President Muhammadu Buhari took power on May 29.
Nigeria police said four other people were injured in the attack.
The explosion was timed to go off as merchants were closing shop, others were hurrying to make last-minute purchases and commuters were catching tricycle taxis home.
Nigeria’s Ministry of Defense denounced the report as “biased” and another attempt by the organization to “blackmail” the military hierarchy.
The Nigerian military must be investigated for participating in, sanctioning or failing to prevent the deaths of more than 8,000 people murdered, suffocated, and tortured to death,” the report said.
An armed fighter with his face covered by a scarf claims Boko Haram still holds several northeastern towns, It says thousands of fighters remain in a north-eastern forest stronghold.
The explosion on Saturday killed people who were prostrating themselves for afternoon prayers outside the mosque, including traders from the nearby crowded marketplace in the largest city in Nigeria’s troubled northeast, survivors said.
Buhari’s election win was Nigeria’s first democratic transfer of power. He inherits a host of problems from his predecessor Jonathan, whose 10 year tenure was marked by aimless security.
UN children’s agency said women and children have carried out three-quarters of all reported Boko Harem suicide bombings with girls blamed for nine such attacks since July.
The assault was the first on Maiduguri for three months and came after sweeping offensives against Boko Haram strongholds.