Three people were shot at during the prayers at Gomari ward in Maiduguri, killing two, while a third person was receiving treatment at the University of Maiduguri Teaching Hospital.
The attacks have raised fears that Boko Haram, a radical Islamist sect behind an uprising last year that led to clashes with the security forces in which hundreds of people were killed, is trying to stage a return.
Malam Abdullahi, who witnessed the attack said: “The assailants drove to the Gomari Mosque on motorcycle taxis and fired at worshipers instantly killing two while wounding the third.”
He said the other worshippers abandoned prayer and ran for cover. The wounded victim was then rushed to the hospital.
Police spokesman, ASP Lawal Abdullahi said they were aware of the killings and senior officers were at the scene.
Boko Haram, whose name means “Western education is sinful” in the Hausa language, wants sharia (Islamic law) more widely applied across Nigeria, which is roughly divided into a mostly Muslim north and largely Christian south.