Registrar of Societies has deregistered Pastor Ezekiel Odero's Newlife Prayer Centre and Church and five other churches in the latest crackdown by the government.
Other churches deregistered include Helicopter of Christ Church, Theophilus Church, Kings Outreach Church and Goodnews International Ministries.
In May this year, Pastor Ezekiel had moved to court to stop the registrar from canceling the registration of his church.
Odero expressed concerns that the Registrar of Societies had threatened to cancel the registration of his church, a move that they said was meant to deny him and his congregation the freedom of religion.
Helicopter of Christ Church is run by Thomas Wahome. He was recently accused of grabbing Nairobi Dam land. Kings Outreach Church broke away from the umbrella churches associated with Prophet David Owuor.
Goodnews International Ministries is owned by controversial Shakahola cult leader Pastor Paul Mackenzie.
Theophilus Church has facilities in Githurai and Njatha-Ini run by Bishop John Githiri and Rev Rachael wa Kuria. The church is among those under probe over claims of cultism.
"In exercise of the powers conferred by section 12 (1) of the Societies Act, the Registrar of Societies cancels the registration of the societies specified in the first column of the Schedule, with effect from the respective dates specified in the third column of the Schedule," Registrar of Societies Maria Nyariki said.