Worshippers were preparing for the mid-morning sermon when police ordered everybody to evacuate the building.
Nairobi PPO Anthony Kibuchi, who led the security agents including those from the General Service Unit (GSU) and anti terror unit, said they received a tip off from one of the church members who said there was a suspicious man in the congregation.
“We got information that a suspicious character was among the congregation and we could not take chances”, Mr Kibuchi told reporters at the church compound Sunday.
He said officers conducted security checks in and around the church and found it safe.
“We have done our checks and I can say that the place is safe for the church sermons to proceed.”
Those who had been evacuated were later screened and allowed into the church.
The scare comes days after Police Commissioner Mathew Iteere had cautioned Kenyans to be alert and report any suspicious characters to the police amid fears of an impending attack over the festive period.
Somalia militia Al-Shabaab Kenyan sympathisers are said to have targeted churches, shopping malls and clubs among other places likely to be frequented by the public.