The government has shut down Precious Talents School in Dagoretti and Pama Academy in Kangemi due to their substandard learning structures.
Education Cabinet Secretary George Magoha said the government has also withdrawn operating licenses for both schools and ordered their pupils transferred to nearby public schools.
The two learning institutions join St Catherine Bombolulu Primary School in Kibra whose registration has also been revoked.
Precious Talents School will remain shut and the 800 pupils enrolled in the school distributed to neighboring public schools.
The closure of the school will see the government transfer 480 pupils to Ngong Forest Primary School, 180 pupils to Jamhuri Primary School and 130 pupils to Riruta Satellite Primary school.
Pama Academy in Kangemi has also been ordered shut by the government with 472 pupils being distributed to New Kihumbuini and Kihumbuini primary schools in Kangemi
The government has also revoked the license of the St Catherine Bombolulu Primary School situated in Kibra over unsound structures.
The government further accuses Non-Governmental Organizations which it says were irregularly funding private schools.
Meanwhile, Nyeri resident Patrick Mwaniki presented a petition to parliament seeking the establishment of a statutory Fund to facilitate compensation of victims of natural and man-made disasters.