No group has claimed responsibility for the attacks. Government officials have not responded to the BBC's requests for comment, but a press statement issued on Saturday by Senator Ali Ndume of Borno South said at least 42 children had been abducted from two schools. BBC reported.
The kidnappings took place at the town's Government Day Secondary School, Mussa Central Primary School, and State Universal Basis Education Board (SUBEB) Secondary School.
Some reports suggest the attacks bore the hallmark of Boko Haram - the Islamist group vying for control over the region against its rival faction, Islamic State West Africa Province (Iswap).
Nigeria is currently grappling with a spate of mass abductions by a range of culprits.
Locals in Borno state have endured decades of insecurity. These latest attacks have prompted some resident of Mussa to flee the area.
Yet traumatised parents have told the BBC they feel they have no choice but to wait in anguish for news about their children.
One man, who did not want to be named for fear of reprisal, said his wife was inconsolable after their six-year-old daughter was snatched away by the gunmen.