Officials claim the church is operating a mental hospital without proper legal documents.
The department has also asked the court to order the detention of Father Pesa as well as the relatives of the patients detained at the church.
They want the cleric charged with nuisance under the Public Health Act.
In their petition, they said the confined people have been living in deplorable conditions.
According to records, the church had about 120 people but the number has reduced to 30.
Principal Magistrate Fatuma Rashid set the hearing date for this Friday.
In his response to the case, Pesa conceded that SOO was taken to the church for spiritual prayers on July 2, 2017, and was in their custody until May 2019, adding that there is no medical evidence to prove that he was tortured.
During a raid by police at the facility last week, some of the inmates confined at the facility begged to be released and claimed they have been subjected to terror.
One of the victims, Millicent Atieno, begged journalists and police officers to remove her from the church and claimed she had been tortured.