The angry youths also set the church ablaze following the protest over a missing one-year-old boy during church service in November.
The little boy, Gold Kolawole, was kidnapped in the church and his whereabouts were unknown till the present moment and it was alleged that the police were not conducting a proper investigation on the matter.
It was gathered that the residents of the area got angry when some pastors of the church started morning service on Wednesday.
They attacked the church and one of the policemen manning the place was mobbed. They alleged that the church was not showing remorse about the missing boy.
The pastor of the church, Prophet Alfa Babatunde, was said to be in the custody of the Directorate of State Service.