A primary school in Kisii was on Tuesday closed and 600 pupils sent home by the institution's sponsors.
The district education boss, Mr James Ochieng, said three priests from the Kisii Catholic Diocese stormed Bobaracho Primary School and ejected the headmaster, Mr Joel Nyangau, saying he was not a member of their church and was least qualified to head the school. The headteacher was posted there this month.
The priests then ordered the pupils to go home until further notice.
A year ago, the church closed five secondary schools and demanded the transfer of the principals, which the ministry did.
During the Bobaracho incident, the priests accompanied by the diocesan education secretary, Mr Chris Osinde, told parents who had gone to protest at the ejection of the school head that the church had not been consulted before the changes were made.
But yesterday the education official accused the church of frustrating his efforts to manage education in the district.
He termed as misguided and the highest degree of arrogance the decision by the church to close the school without consulting his office.
"The incident is ill-timed as Kenya Certificate of Primary Education exam candidates need these final days to prepare for their national examination, which is only two weeks away," he said.
He said he would take up the matter with Bishop Okemwa Mairura.
Recently Nyanza education boss David Siele accused the Kisii diocese of meddling in the management of schools, leading to poor academic standards.