Machogu said this trend may continue for a while until details of these learners are fully and accurately captured.
He singled out controversies and the inconsistencies around learners' birth certificates as the cause of some learners living on capitation money of their colleagues.
Machogu said in some cases, serial numbers of birth certificates are shared among learners, raising questions on the accuracy and thoroughness of NEMIS data.
Machogu also said that in some instances, birth certificates are missing, hence incomplete registration of students' data in the government system.
The effect is that these learners are feeding and using resources courtesy of other learners whose data have been captured and receiving government capitation.
Secondary schools heads on Tuesday revealed that there exist thousands of students carried by the weight of those who receive capitation, another development that leads to financial crises in schools. Through their associations' chairman Kahi Indimuli, the heads said that schools are forced to keep students in school at the expense of others.
''We continue keeping the students in schools because learners cannot send them away because the mistake of funding may not be of their making. They have to feed on the same food of those who have been funded,'' Indimuli said.
Indimuli further said the challenge boils down to schools with small populations which are forced to reduce the ratio of service delivery to learners.
''You can imagine having 200 learners who are not funded in a day school of 500 students with no other source of funding away from capitation, It becomes a big headache,'' he said.
Jitters over JSS: Government demands all student details in NEMIS
Indimuli further said schools continue to incur debts on services rendered to students at the expense of government mistakes.
''There is something which is not right with issuance of birth certificates and serial numbers. If they decentralize issuance of these documents, let there be a way to identify serial numbers with Counties where the services are offered,'' Indimuli said.
Appearing in Parliament last week, Machogu said some schools are only funded depending on the number of learners fully registered in the government data bank.
''The ministry provides capitation to learners who are fully registered on NEMIS, that is, those who have birth certificates and parents' details. Because some learners are in school but are not fully registered on NEMIS, there is the risk of under-capitalisation in some schools,'' Machogu said.
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He clarified that all learners are registered however, only with requisite documents are fully registered which enable them access to government services.
''The NEMIS allows for the registration of both learners with and without birth certificates. Those with birth certificates are fully registered while those without birth certificates are partially registered,'' he stated.
Teso MP Mary Emase pressed the CS to outline measures put in place to ensure that children from needy households who cannot afford the lunch fee programme to remain in school and enjoy nutritious meals.
''The leadership of Junior Secondary Schools oblige to ensure that no child drops out of school as a result of failure to pay lunch fees, which in most schools is Sh15,000,'' Emase said.
Machogu said feeding learners in school is the parents' responsibility noting that the capitation stands for tuition fees only.
''The capitation that is currently available under the Junior Secondary programme is limited to the tuition component,'' Machogu said.