Both Christian and Muslim leaders denounced the new proposals.
Earlier in the month the Kenyan government published new rules that require religious leaders to have theological degrees and religious groups to submit a statement of faith.
The rules among rising concerns of corruption among some church leaders and radicalisation among some imams.
The government also wants to stop a growing trend where Christians send their offerings to pastors via mobile phone, and has expressed concerns with TV preaching.
Speaking to The Washington Post Bishop Philip Anyolo, chairperson of the Kenya Conference of Catholic Bishops, said: "Similar attempts to regulate the procedures for Christian marriage have led to a major drop in young people coming to church to celebrate the sacrament."
Earlier in the week church leaders from different denominations threatened countrywide protests against the rules.
Around 1,000 religious leaders gathered for a meeting in the capital Nairobi to fight against the rules, which they're labelling religious persecution.
Bishop Mark Kariuki, chairperson of the Evangelical Alliance of Kenya, said: "Requiring pastors to obtain a theological degree is presupposing that all ministers of the gospel are learned.
"There are some who are called and yet do not have the benefit of formal education."
He also claimed that no churches were formally registered in 2015 and that in 2014 more than 7,000 churches were denied recognition by the authorities.
"This is manifest discrimination and persecution of the church.
"We will not take it anymore."
Sheikh Adan Wachu, chairperson of the Supreme Council of Kenya Muslims, also warned the government that the regulations would violate freedom of worship and believe.
