Principal Secretary for Basic Education, Prof Julius Bitok, has urged parents and guardians to help their children in the selection of pathways and subjects.
In contrast to many other schools weighed down by congestion and inadequate resources, more than 1,000 schools in Kenya have fewer than 10 learners each.
The ongoing verification exercise, which is due to end today, has also revealed that 25 junior schools have just one pupil each, with several teachers assigned to each school.
The Basic Education Principal Secretary, Prof Julius Bitok, said that the findings raise serious questions about the optimal use of resources.
The audit of public schools aims to clean up school and enrolment data. By Tuesday, over 20,000 schools had been verified out of more than 30,000 public schools.
Prof Bitok confirmed that the verification exercise, set to conclude on Friday, was initiated following a damning audit report by Auditor General Nancy Gathungu, which exposed the loss of billions of shillings intended for schools to fraudulent institutions.
The June report revealed that the government had overfunded schools by Sh3.7 billion between 2020 and 2024 through fictitious institutions and inflated enrollment numbers.
"The exercise was prompted by a 'damning' report from the Auditor General that revealed funds were not reaching the intended schools,” Prof Bitok said during an interview with a local TV station.
However, the PS urged Kenyans to begin a candid conversation on schools with the lowest enrollment for the optimal utility of resources. Prof Bitok questioned the efficiency of maintaining such institutions.
"Is it really optimal utility of natural resources to have a school with only one learner with a number of teachers?" asked the PS.
He stated that county directors have been tasked with engaging stakeholders to understand the reasons for the low enrollment and the challenges facing these schools.
However, he assured principals and other education stakeholders that the ministry aiming to disburse Sh17 billion in capitation funds next week once the audit is complete. The verification will be concluded by Friday, September 5.
The PS also confirmed that the first batch of capitation funds was released last week after the ministry received the disbursement from the National Treasury.
"We are on track to ensure the right number of learners are getting this capitation," he said, adding that the ministry is "verifying all the learners in each school, the school accounts and everything for the purposes of capitation."
The PS said the Ministry of Education is conducting the comprehensive audit of learner data, school accounts, and total school numbers to ensure capitation funds are disbursed accurately.
Prof Bitok added that the audit would also address the perception in the public eye that the ministry is failing to disburse funds to the correct schools.
The PS said that by this Friday, all schools, with support from sub-county and county education directors, will have completed the verification to confirm the accurate number of learners, institutions, and their accounts.
The Ministry of Education is also replacing the National Education Management Information System (NEMIS) with a new, centralised platform known as the Kenya Education Management Information System (KEMIS) to combat widespread fraud in capitation funding.
Prof Bitok stated that KEMIS will be a "game-changer," leveraging technology to capture data on all educational institutions from early childhood to higher education.
The ministry previously used NEMIS, a system school heads complained about due to its inefficiency and inability to capture all learners, especially those without birth certificates. This inefficiency was exploited by officials to provide inaccurate data and steal capitation funds.
