Timothy Lentuda of Jipor ministries in Maralal town is detained at Maralal police station.
He was arrested at his house on Friday afternoon.
Samburu central Officer commanding Police Division, Abagaro Guyo said that they arrested the pastor after it was reported that he had impregnated one of his church members.
Guyo said they are investigating the matter and Lentuda would be taken to court once investigations are complete.
Members of the church flocked maralal police station, formed small groups and spoke in low tones.
They said they could not believe that a man of God would do such an ungodly act.
"I can't agree with that, my pastor cannot do such," said a member.
Dorcas Lemedeket, a bishop at the church said that the matter is set up by other struggling churches.
She said that other pastors who have not been able to attract huge crowds are jealous of pastor Lentuda.
Lemedeket added that the plot would not work adding that they would do a DNA test once the minor gives birth.
"We know there are some churches behind this, its out of jealous that they are trying to taint the image of our church and that of our apostle," she said.
Samuel Lenkulate who is the guardian to the minor said that the man of cloth had promised to marry the minor but dumped her when she was six month pregnant.
"We, as a family, decided to report this matter when we heard that the pastor had arranged for a wedding with another member of his church," he said.
Lenkulate said that the minor is a 17 year old girl.