Confirming the incident, Naivasha OCPD Benjamin Boen said that they received reports that some people wanted to burn the church for radicalizing area youths.
The senior officer was however quick to note that the allegations of forced fasting and radicalizing of the youths could not be confirmed.
"It appears that some members who left the church which is legally registered are unhappy and are fighting the current leadership," he said.
He said that the information they received was that the church was forcing the members to fast while others were detained against their will.
"On receiving the information the area security team moved in and arrested the 12 who included the owner and the wife but some of the allegations are not adding up," he said.
He added that they had summoned the persons who had tipped the police with the incident so that they could clarify the information.
The incident comes a couple of days after police intercepted 55 Ugandans who were on their way to Ethiopia for an evangelical mission.
The group from Christ Disciple Church (CDC) included 29 adults and 26 minors who did not have proper travel documents before police moved in.
In the last couple of weeks, the country has been awash with news of cultist organizations with police recovering over 100 bodies of members of Good New International Church in Shakahora forest in Kilifi.
The church leader Paul Makenzi Thenge is in police custody while another preacher Ezekiel Odero of New Life Prayer Center and Church is also in court facing various charges.