Some members of the clergy have come out to defend the integrity of the church following condemnation stemming from Shakahola massacre.
They said churches are self-regulated and the government should not make blanket condemnation.
Instead, the clergy, under "Church Umbrella Bodies", faulted the State for laxity that led to the deaths at Shakahola.
Bishop Stephen Mutua, the chairman of the Kenya Coalition of Churches Alliance and Ministries, said churches operate within the confines of the law and have internal mechanisms for dealing with cases of indiscipline involving members.
He exonerates the church from the blanket condemnation and resultant push for scrutiny based on the Shakahola massacre executed by controversial preacher Paul Makenzi, of Good News International Church.
"All our churches are regulated by the Societies Act and every church is self-regulated under their individual constitutions. Separation of church and State is a principle embraced by secular countries all over the world, concurrent with the provisions that there shall be no State religion,'' Dr Mutua said on Friday during a press briefing in Nairobi.
The pastors distanced themselves from the estranged pastor, Makenzi, saying he has never been part of their umbrella bodies.
"It is important for Kenyans to understand that except a few people masquerading as pastors, Christ's church is not in a crisis and no one should scare Kenyans to deal with us contemptuously always," he said.
Church and Clergy Association of Kenya chairman Hudson Ndeda scoffed at Interior CS Kithure Kindiki for demeaning the clergy.
"Hon. Kindiki, we are not happy with the way you address pastors and the way you address church matters. Please restrict yourself to Makenzi. And since we respect you, when you talk about pastors and the church, please speak with due respect," said Bishop Ndeda.
He, however, clarified that the church should not be seen to be at war with the government.
''We don't think the government has refused to listen to the church. That is the reason President William Ruto formed a commission to investigate this matter. He has made a commitment that he wants to listen to us and the task force is not meant to take away the freedom of worship and religion in the country,'' he said.
Deliverance Church of Langata Bishop Geofrey Njuguna wondered why the government cannot differentiate between genuine churches and cults.
He said since churches remit returns to the government, it is its responsibility to ensure no religious leader abuses freedom to exploit Kenyans.
''Trying to create an impression that pastors cannot be trusted is mischievous. You should not base on what happened in Kilifi to indicate that pastors are not trustworthy is unfortunate," said Bishop Njuguna.
