The deaf teacher reportedly committed the offence through the help of a 10-year-old student of his.
His arrest was facilitated by a non-governmental organisation, National Council of Women Society (NCWS), who reported the matter to the security agency.
Muhammad Gidado Fari, the state commandant of the NSCDC revealed this in a statement he released to the press.
According to Fari, a 10-year-old student of his helped deliver the baby to the accused, who subsequently defiled it.
The deaf teacher has however denied any involvement in the rape, despite being identified by the student.
Daily Post reported that the matter has been transferred to the Ministry of Justice, for more resources on the case.
Meanwhile, the baby has been taken to the University of Maiduguri Teaching Hospital for observation.