The situation is worse for day schools where some principals claimed they received as little as Sh400 per student for tuition.
This means the financial crisis the instutitions are grappling with is far from over despite the disbursement of Sh28 billion capitation funds by the government last week.
In Nyanza, a number of schools claimed the amount they received will only be used to offset salaries of non-teaching staff as well as pay part of their debts as they ponder on their next move.
At Kiabonyoru Mixed High School in Nyamira, only Sh2,000 per student was available against expectation of around Sh11,000.
Principal Richard Ariemba said the school will have to send home learners who are yet to clear the school fees to collect fees. He claims the school has debts of Sh8 million.
"It is still difficult and going with the situation, we are going to force parents to buy exercise books for their children because we cannot sustain the budget for stationery which has been severely hit by reduced fee payment as well as the irregularly disbursed capitation," Ariemba said.
Zablon Awange, Kisumu's Executive Secretary for Kenya Union of Post Primary Education Teachers (Kuppet) said their members were expecting 50 per cent of annual capitation funds for first term but have received less than half.
In Mt Kenya, a school in Laikipia county received only Sh48,000. This despite the institution struggling with debt, including Sh700,000 for exercise books and learning materials.
Kenya Secondary School Heads Association Chairman Kahi Indimuli said he was aware of the disbursement of the kitty.
"There is disbursement of the money to schools, but we are yet to receive the circular of the distribution of the funds," said Kahi, also the Principal at Machakos Boys School.
At Muthithi Secondary School, the Principal Mr Njenga Gathige said the amount allocated for the tuition should be increased to help cater for the urgent needs as the tuition account got Sh300,000 as compared to the operation account with Sh2.4 million.
Njenga said the Day secondary schools are highly affected as the majority depends on bursary kitty from the county and NG-CDF owing to the poverty levels in the rural set up.
"We appreciate the allocation but it will expose the schools to more challenges as there are suppliers who have been waiting for the payments," said Njenga.
He added that the school pays salaries to a tune of Sh470,000 per month.
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Gititu secondary school principal Mr Caesar Njoroge said the amount disbursed would only pay the salaries for the school employees.
"We are completely lost as we expected each child to get an allocation of Sh11,000 only to get Sh3,000. The amount is hardly enough to support school programmes," said Njoroge.
Dol Dol Boys Secondary school head David Kimani said the amount disbursed was 'peanuts' to management of the school operations.
"The amount allocated is little but we are awaiting for the circular from the Ministry of education on the same," said Mr Kimani.
In North Rift, section of heads who spoke to The Standard in confidence also said the minimal amount released was demoralizing and that some of them were no longer interested of holding the principal post.
"We received only Sh400,000 in our tuition account against a population of over 1,000 students. We are yet to receive a circular for us to know each vote head for the allocation but this is just a drop in the ocean. It is not even 50 percent of the first term," stated a school head.
The principal said debts are accumulating while needs including stationery, chemicals for laboratory practicals among others keep increasing as inflation escalate.
The principal further said the task of running institution is becoming a burdening task since they have been managing on growing financial deficits.
Capitation queries: Schools say funds released by government are too little
Another principal said the trend of partial payments is not the best, saying issues affecting schools are not well addressed.
"The government is not committed at fully addressing financial needs yet it is inciting parents against meeting their financial obligations. In our school, only 15 percent of parents pay and clear school fees but 85 percent pay the way they want," added the principal.
This, the school head added, makes it difficult to manage schools without finances.
And lack of birth certificates to list learners on NEMIS is even making funding in Turkana more worse as schools receive minimal allocations.
Perer Epukon Loyapan, the Turkana County Kenya Union of Post Primary Education Teachers (Kuppet) Executive Secretary said 'the amount we receive is not worth the need'.
"Funds received were too little and most principals are at a threat of being taken to court by suppliers of goods and services over delayed payments," said Loyapan.
He claimed that in some secondary schools, students received allocations as little as Sh2,000 each for operations and Sh300 for tuition.
In Western, a section of the school heads interviewed indicated that they were struggling to manage their institutions as a result of the meager disbursements by the Ministry of Education.
The Sacred Heart Mukumu Girls Principal Sister Jane Mmbone said her school was allocated Sh3,727 capitation per student stating that the money is far way below.
"To be honest things are tough, we have received the capitation but we have been allocated Sh3727 as a capitation per student from the usual Sh11,000, we have to look for other alternatives to meeting our daily expenses to ensure the normal operations of the school are not interrupted, "said Mmbone.
She said that her school has not paid the suppliers and "we are planning to raise some money when the students break for half-term by ensuring parents pay fees balances."
In Busia, Bishop Obiero mixed school principal Kennedy Oguta said they have received some funds from the Ministry.
Mr Ogutu said he ventured into agricultural projects like growing indigenous vegetables, sukuma wiki, and even poultry farming to supplement what the Ministry disbursements.
"We are yet to get the circular from the Ministry of Education but as a school, we decided to have a board meeting where we decided to borrow.
[Reports by Titus Too, Boniface Gikandi, Stanley Ongwae, John Shilitsa, Olivia Odhiambo and Anne Atieno]