In a Facebook live video, RCCG General Overseer, Pastor Enoch Adeboye, was seen leading a church service.
Those in attendance were less than 50.
Adeboye prayed that God will help the world overcome the disease and called for fervent prayers.
Lagos State had ordered that all religious gatherings must not have up to 50 worshippers in attendance.
RCCG, in its reaction, instructed its branches to obey the directive.
It advised those with the capacity to run more than one service to ensure members do not exceed 50.
Nigeria has now officially recorded 25 cases of the deadly disease.
The country has also restricted international flights to Lagos and Abuja.
Meanwhile, the Lagos State Government has set in motion a clinical trial to confirm the efficiency of chloroquine as a treatment for coronavirus.