The archbishop expressed disappointment that the same government was more focused on regulating churches and crucifying the clergy instead of dealing with the real issues in Kilifi County.
"Families lost their loved ones and some are unsure where their kin are. The government is not focused on them but is busy thinking of how to punish other churches," said Kivuva during the ordination of Rt Rev Cleophas Oseso as the fourth Bishop of the Catholic Diocese of Nakuru on Saturday.
The bishops said the Shakahola incident was criminal, and it was time for Kenyans to join hands and support relatives of those killed and the missing.
Kivuva said it was the government's duty to deal with individuals who use the pulpit to sacrifice, cheat and steal from the congregation.
"It is time for the government to punish those involved instead of beating around the bush by targeting innocent clergy, Imams and churches," he said.
Instead, Kivuva told the government to focus on resolving the economic hardship that has led to the demonstrations by the Azimio coalition.
He said the only option for prosperity was dialogue. "We are going through challenging times, but we are the only ones who can build or destroy Kenya. We applaud the Kenya Kwanza and Azimio teams for embracing talks".
Deputy President Rigathi Gachagua said the church should not be indiscriminately condemned over the deaths.
The DP said the government would deal with those responsible for the over 100 deaths, and would not allow culprits to get away with it.
"What happened in Kilifi by whatever name is unacceptable. And the government will not allow anyone to hide behind the pulpit and the church of Christ to commit crimes. Criminals will be dealt with as criminals in accordance with the laws of the country, the Penal Code and the Criminal Procedure Act.
"It is not right; I want to urge those who are talking about Kilifi not to condemn the entire church of Christ and all the pastors. The church is a reflection of society, the membership is a reflection of the society, congregation is part of the society. What happens in society is the same thing that happens in the church," said the deputy president.
Gachagua called on churches to help keep youths away from drug abuse and alcoholism by mentoring them.
Archbishop Bert van Megen, the Apostolic Nuncio to Kenya and South Sudan, installed Bishop Oseso. He warned that Kenyans must learn from what is happening in Khartoum, Sudan.
According to Archbishop Megen, Kenya will only move forward with dialogue and not violence, and urged politicians to come together, talk and come up with solutions.
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Megen said that the Catholic Church was happy with Bishop Oseso and believe that he is the right person for Nakuru. Oseso, on his part, said he was humbled by the appointment. "The church will partner with the government in matters of education, health and economy, but will keep its sanctity".