Kakamega Primary School, where 15 children died following a stampede on February 3, has stopped nine churches from conducting Sunday services there.
Police directed the school's board of management to stop the services amid pressure by local leaders for the decision to be taken.
During prayers and a cleansing ceremony at the school on Monday, a handwritten notice stated that the school was out of bounds for churches.
A day after the incident, former Kakamega Senator Boni Khalwale asked the Ministry of Education to stop churches from conducting prayers at the institution.
This sparked fury, with clerics demanding an apology, saying the politician linked the incident to religious groups.
Headteacher Dickson Wanyangu said on Thursday that details on the decision and the churches affected were kept private but that meetings with their heads would be held and the move explained.
“This is a decision made by the board of management. No church will be allowed in the compound,” he said.
''The situation has remained disturbing but we leave everything in the hands of God."
The Nation established that the religious groups were not paying any levies to the school for use of the premises.
So far, police have taken statements of 16 teachers as part of investigations into the tragedy, amid calls for a quicker process.
Western Region Criminal Investigations Officer Shem Nyamboki said detectives were planning to record statements from pupils and other witnesses.
The recording of pupils' statements was put off on Thursday to allow counselling by a county team and St John's Ambulance personnel.
Learning has resumed, with 3,038 primary pupils and 184 in the ECDE section returning to school following its reopening on Monday.
But Mr Wanyangu said some of the pupils, especially those in Standard Four and Five, and some teachers were yet to come to terms with the tragedy.
The detectives will forward the investigations file to the Director of Public Prosecutions (DPP) for perusal, who will recommend action based on evidence gathered.
There is the possibility that the DPP will recommend a public inquest before a magistrate.
Should this be the case, the magistrate will determine the next course of action, based on the findings from testimonies.
Mr Nyamboki said preliminary investigations indicated teachers restricted pupils to use of just one staircase and reserved the other for themselves.
“The investigations are progressing well. We are trying to establish whether there was negligence on the part of teachers and whether the evidence on record can support criminal culpability on their part," he said.
Western Region Police Commander Peris Kimani said the investigations were at an advanced stage.
On Monday, parents Irene Ambundo and Ibrahim Kiverenge called on the government to expedite investigations and make the findings public to end speculation.
“There is a lot of speculation concerning the death of our children. Parents, more than anybody else, are eager to know what led to the deaths,” said Ms Ambundo.
Speaking at the burial of her daughter, Prudence Elizabeth, at Upukhulu village in Navakholo on Monday, Ms Ambundo said her children had been complaining of slippery staircases in the three-storey building.
She said they also complained of strange beings appearing and scaring them.
Some pupils said a teacher directed them to use the stairway on one side of the building while others claimed the stampede occurred after some blocked the way on the second floor of the building.
Mr Kiverenge, father of Naila Kiverenge, urged the public to stop speculation on the incident and await the findings of an inquiry.
“It is hurts whenever we read unconfirmed reports about the cause of the stampede on social media. Please give us a break. Give us time to mourn our children peacefully and let investigating authorities do their work and tell us what happened,” he said at the burial of victim Joseph Musami in Ikolomani.
He said parents were saddened and disturbed by the fact that what was supposed to be a safe haven for their children turned out to be a death trap.
“The damage is immeasurable and irreversible. We want to know what killed our children at a school where they have been learning for years,” he said.
Additional reporting by Dianah Shimuli