Thousands of protesters have stormed the Lagos branch of the Commonwealth of Zion Assembly (COZA) and its headquarters in Guzape, Abuja.
The allegation caused a storm over the weekend with many calling for the pastor’s arrest and others showing their support for the preacher.
Fatoyinbo said he had never raped anyone not even as an unbeliever.
Protesters on different divides of the rape allegation clashed on Sunday despite the army and the police deploying officers to the locations.
Pro-Fatoyinbo protesters temporarily disrupted a sit-in organised by enraged Nigerians against Fatoyinbo in Abuja.
A police van later moved in to protect the anti-Fatoyinbo protesters.
One of the anti-rape protest organisers, Abiola Akiyode-Afolabi, said the security agencies have a responsibility to protect civilians at the protest ground.