The Ministry of Education has also been retaining about Sh1,979 per child, further chopping the yearly allocation for learners in public schools.
In the end, schools only receive Sh15,479 from the government, from which they are again expected to deduct another Sh5,000 to fund infrastructure.
The details are contained in a petition sent to parliament by the Kenya Secondary Schools Heads (Kessha).
"Once schools receive the disbursement from the ministry, they are then required to set aside Sh5,000 for the infrastructure fund. This leaves secondary schools with an average of Sh10,479.37 per child to run operations in schools," reads the petition.
Cumulatively, secondary school heads argue they are owed Sh54 billion by the government, frustrating smooth running of schools and payment of suppliers.
The revelations come in the backdrop of the Ministry's pronouncement that it had released all funds owed to schools in September.
Education Cabinet Secretary Ezekiel Machogu last month said that the government had released all capitation funds owed to schools.
"To ensure the normal running of all school activities, the Ministry of Education has received Sh16 billion as capitation funds from The National Treasury for disbursement to learners in public Primary, Junior and Secondary Schools," Machogu said.
However, a petition to parliament by the Kenya Secondary Schools Heads (Kessha) on Thursday paints a grim picture.
The petition is addressed to the Clerk of the National Assembly and copied to the Speaker of the National Assembly Moses Wetangula, and the Speaker of the Senate Amason Kingi and is dated October 31.
Lifting the lid on the funding challenges in schools, the heads have revealed that over the past five years, the ministry has been disbursing an average of Sh17,458 per child.
In the report, they say in 2019 alone, the government did not send Sh3,167,804,931 of the total capitation to secondary schools.
Breaking down the disbursements, the report by the heads explains that in the first term of 2019, the government disbursed half of the Sh22,244 translating to Sh11,122 per child.
In the second term, schools received 14.91 per cent instead of the 30 per cent, translating to Sh3,315.62 per child.
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The third term, disbursement was however 30 per cent translating to Sh6,679.31.
Cumulatively, the schools received 94.94 per cent of the total capitation, leaving a deficit of 5.06 per cent.
And the heads say this translates to Sh3.2 billion, which they say should have been sent to the schools.
But this was the start of a funding mess that rolled over for the next five years, leading to a back-and-forth accusation between school managers and the government.
What further aggravated the funding crisis was a change in the disbursement plan that adopted a financial year formula instead of the previous model of the school calendar.
And this, according to heads, expanded the funding gap.
In 2020/2021 financial year, schools did not receive Sh16,982,119,448 translating to an average of about Sh5,000 deficit per child.
In the 2021/2022 financial year, the amount owed to schools was Sh15,968,967,196 or approximately Sh4,451 not sent to each student.
The biggest deficit, however, was recorded in the 2022/2023 financial year, when the amount owed shot to Sh18,101,294,280.
This translated to some Sh4,905 per child, not remitted to schools.
Collectively, the report by the secondary school heads stands at Sh54.2 billion.
The report explains that the funding mess started in 2018 when the National Treasury retained a fraction of capitation money meant for schools.
It emerged that of the Sh22,244 expected to fund each student, the national Treasury only released Sh17,458, citing lack of funds.
The report notes that the Ministry of Education in turn only remits Sh15,479 to schools, retaining Sh1,978 per student for the school medical cover, textbooks, co-curricular activities and SMASSE.
Once the money is sent to schools, the report further says that another Sh5,000 per child is slashed and set aside to cater for infrastructure development.
This means that the actual amount that remains per child is Sh10,479.37 to cover operational expenses within public schools.
Appearing before the National Assembly Education Committee on Wednesday, Machogu said the situation has been brought about by the fixed allocation to the ministry in spite of the rising student population, noting it could worsen next year with the expected increased enrolments.
Machogu said the current secondary school population is 3.9 million learners against an available budget of Sh65 billion this financial year.
He said this amount is below the approved Sh22,240 per learner, leaving a funding deficit of Sh22 billion.
"Next year, we project that the enrollment will be 4.2 million learners. If the funding remains as it is, the capitation will reduce to Sh15,476 per learner," said Machogu.
The admission of the funding crisis in public schools came weeks after the ministry and secondary school heads engaged in open spat over free education money.
And teachers' unions also waded in the matter, faulting the ministry of late disbursements and withholding money meant for schools.
The ripple effects of the financial challenges, the school heads say, have forced schools to lay off teachers employed by their boards of management (BoM), leading to reduced quality of education.
"Due to financial constraints, several schools are unable to adequately provide resources necessary for undertaking practical lessons, especially in the sciences," the petition reads.
They also argue the funding shortfalls have limited access to sports, arts, modern agriculture and clubs that enrich students' educational experiences and provide avenues for careers in those areas.
In their recommendation, school heads now demand the vacation of the directive to retain infrastructure funds from capitation.
"As a result of underfunding, accrued deficits, and the requirement to retain an infrastructure fund that cannot be utilized for school operations, these schools are facing significant financial difficulties. These shortfalls have had a profound impact on their ability to provide a quality education to their students, compromising their teaching and administrative functions," the petition reads.
School heads also demand a review of capitation every three years to factor in inflation.
They are also demanding a review of the boarding and lunch fees to factor in inflation.
They also want students exiting secondary school with fees arrears to be compelled to pay.
"The Ministry of Education should advise schools on measures to take where Form 4 students exit with fees arrears. At the moment, schools are stopped from withholding Form 4 certificates as a method of ensuring collection of fees arrears," the petition reads.