A church at the centre of a land tussle was destroyed on Wednesday night at Jogoo area in Kisii Town.
Church officials said hired goons descended on Millennium SDA Church and vandalised it.
The church has more than 1,000 members and it cost them more than Sh800,000 to put up the structure, church elder Joseph Otwori told journalists on Thursday.
He said he was woken up at 11.30 pm by a guard at the facility.
"I immediately mobilised some members who rushed here but they found the thugs escaping through the back gate," Mr Otwori said.
He condemned the destruction.
Mr Otwori said the court had not given any orders for the church's demolition and expressed surprise at the turn of events.
"The case has been in court and it granted us the status quo until the matter is determined legally," he said.
Kisii County Assembly Speaker David Kombo, who visited the scene, condemned the raid.
He called for multi-agency investigations into the incident.
"We wish that the culprits be brought to book as soon as possible," said Mr Kombo.
Kisii County Deputy Commissioner Peter Mbugi said there were underlying issues that need to be dealt with between the parties involved in the dispute.
He said the church needs to present its land ownership documents.
Mr Mbugi asked the church officials to report the vandalism so that investigations begin.
"Action will definitely be taken once they report. Let them file a complaint with security agencies so that action will be taken," he told reporters at his office.
The Millennium SDA Church and the Child Welfare Society have been entangled in a court case over ownership of the land on which the church is built.