The bodies of children were among the dead. Police said exhumations are ongoing.
BBC reports the shallow graves are in Shakahola forest, where 15 members of the Good News International Church were rescued last week.
Church leader, Paul Makenzie Nthenge is in custody, pending a court appearance.
State broadcaster KBC described him as a "cult leader", and reported that 58 graves have so far been identified.
One of the graves is believed to contain the bodies of five members of the same family - three children and their parents.