Maiduguri has been at the epicenter of the group's seven-year insurgency.
The militant group launched its first attacks in 2009 in Maiduguri.
Amnesty International says Mohammed may be responsible for mass executions.
The Nigerian president claims Boko Haram has been "technically" defeated despite an upsurge in attacks.
The government has said it cannot guarantee all attacks will stop by the New Year.
The second assault on the city in a week comes as regional powers rally against the terror group.
Media group linked to Nigerian terror group show military camp for young boys in northeastern Nigeria.
Experts fear the Nigerian Islamists, emboldened by the success of ISIS, will soon realise their expansionist ambitions