Scores of others were seriously injured as a house and car belonging to one of the church leaders were set on fire just before the service could start.
The church, Africa Israel Nineveh, run by a family, has been embroiled in leadership wrangles for long after the death of its founder Mr Daudi Kivuri in the 1950s.
Mr Kivuri, before his death, is said to have handed leadership roles to one of his sons, Mr Mweresa John.
However, Mr Kivuri’s widow Mrs Rebecca Kivuri and another son Chadiva Amugune and a section of church members, are said to have fallen out with Mr Mweresa’s leadership style touching off a long battle over the control of the church’s affairs.
Just six months ago, a Kisumu court ruled in favour of Mrs Kivuri but the ruling was not well received by Mr Mweresa.
On Sunday, before the chaos broke out, it is alleged that Mr Mweresa had hired goons to attack the rival group.
It is alleged that he had strategically placed the goons so as to accomplish his mission.
A group of the goons are said to have been hiding in his house, which was set on fire, while another was at the church ready for the their ‘mission’.
However, their plans were thwarted as they were overpowered by the church members who killed three of the alleged goons while many others were injured and rushed to nearby Benja Health Centre and others to Hamisi hospital.
Mr Mweresa, however, escaped as the situation got worse and he is still at large.