Parents of Bahati DEB Solio Primary School in Kieni Constituency have protested against paying Sh600 for a computer room.
The residents, who displayed receipts, demanded an explanation from Education Cabinet Secretary Fred Matiang'i.
They also protested against other charges imposed on them by the school.
Every pupil pays Sh150 for the watchman's salary and Sh500 to cater for school activities, they said.
Galgalo Bure on Thursday said the free primary education had turned out to be a mirage for parents in the school.
"We are paying for the watchman, lunch, toilets and school activities. Parents are really wondering what government officials mean by free education," he said.
Ann Wangui said she transferred her children to another school when they were sent home for not clearing fees.
She said that upon payment, parents were issued with receipts which did not have an official stamp.
Some protesters said nursery school children were also being made to pay despite not being enrolled in the digital literacy programme.
The headteacher, only identified as Mr Kivunja, dismissed the claims, accusing parents of making wild allegations.
"No such money has been collected. If there is any money being charged by this school, then I am not aware," Mr Kivunja said.
Parents said they were asked to contribute Sh250 each for the construction of toilets.
The school, which has a population of 200 pupils, has pit latrines.