The group, led by Pastor Josua Katuman, demanded that the pastor leaves as the church allegedly "belongs" to Katuman.
The faction of the church claimed they had bought land in 2003, and built the church, only for a "strange" pastor to be brought.
They said that they had been barred from worshiping at the church they had built.
The faithfuls who had been inside the church would not be easily chased from the church, causing chaos that nearly became violent.
Police from Kasarani Police Base had to be called to the site, to disperse the mob.
The incident comes barely a week after another church fight in Vihiga turned violent, causing the death of four people.
Video by Citizen TV: