News of the shooting made residents, mostly non-indigenes, to flee their homes in the night and seek refuge at the General Jalo Army Barracks, Yola, for fear of being killed.
It was learnt that the unknown gunmen, who rode on motorcycles, entered the church and opened fire on the worshippers. 11 members reportedly died on the spot and several others sustained bullet wounds.
One of the wounded church members reportedly died later, bringing the number of those who died to 12, even as five others are in critical conditions at the Specialist Hospital, Yola.
Last Friday, 12 mourners were killed in Mubi, the commercial nerve centre of the state by suspected members of Boko Haram sect.
Those killed were allegedly holding a meeting on how to raise money to convey home the remains of three of their relatives earlier shot dead by members of the sect on Thursday before they were attacked.
Police in the state said they were investigating the incidents.