Some 1 million learners were not included in the Free Day Secondary Education programme this financial year.
Another 1.4 million learners will not be factored in the next financial year when they transit to Grade 8 in Junior Secondary School.
Additionally, co-curriculum funding in schools has not been taken seriously despite the government's promise to roll out the Competency Based Curriculum (CBC) in schools.
The government also owes examiners Sh1 billion after marking three examinations last year.
Speaking while appearing before the Parliamentary Select Committee on Education during their budget submission for the next financial year, Education PS Belio Kipsang said the JSS funds had not been factored in this year's budget but funding came through the supplementary budget.
"Out of Sh33.99 billion which is required to finance the transition classes of JSS, we only got Sh15.46 billion. We will have another 1.4 million in Grade 7 as well as 1.2 million learners in Grade 8," Kipsang said.
The PS further said that at least Sh88 billion is needed for the free day secondary. However, the government has only allocated Sh65.5 billion leaving a deficit of Sh24.5 billion.
"Almost one million learners are not factored in the government funding in our day secondary schools. This makes the majority of them drop out of school," Kipsang noted.
The PS said many schools are struggling and it's time that both the national government and MPs should assist to cushion the institutions from derailing their operations.
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‘‘The areas we have identified as key underfunded are critical to the achievement of our mandate. We therefore require addition of Sh42.043 billion and Sh1 billion under recurrent and development budgets respectively,’’ Kipsang said.
The PS said there is a notable increase in the recurrent budget of Sh9.089 billion from the current budget. The main areas of increase are Sh5.887 billion for capitation to JSS, Sh964 million for Free Day Secondary Education capitation, and Sh300 million to cater for Quality Assurance and Standards.
Other areas include Sh173 Million to support Co-Curricular activities, Sh444 Million under Personnel Emoluments for the recruitment of Quality Assurance and Standards Officers, and Sh470 Million for the supply of sanitary towels.
The concern on funding caught the eye of committee members who raised concerns about the underfunding of co-curriculum activities in schools.
"With the new curriculum, the government needs to give priority to co-curriculum activities by injecting more funds as a way of enhancing pathways in schools. Last term, some schools had to pull out of drama festivals and ball games for lack of funds," said committee chairman Julius Melly.
Malava MP Malulu Injendi questioned why the government has continued to be silent on when teachers who had been contracted for invigilation will be paid.
‘‘Examiners who gave their service four months ago have not been paid and no word is coming from the government on when they will be paid,’’ Injendi said.
But the PS promised teachers will be paid soon once the funds are available allaying fears failure the delay will compromise exams integrity.
"Because we have not been paid the allowances, this should not be a way of compromising the integrity of our exams. This year we are going to review rates and ensure our professionals who are contracted for marking and monitoring are adequately taken care of," noted Kipsang.