Rolling out the programme in January, President Mwai Kibaki said free education would ensure that children from poor homes acquired quality education.
His government introduced universal free primary education after he was first elected in 2002.
Under the programme, the government would pay tuition fees while parents covered boarding costs and bought uniforms.
But seven months after the programme was supposed to take off, the government has provided only a quarter of the funding schools need to make it work.
Some school administrators have been forced to run the institutions on a credit line while others have opted to reinstate tuition fees to avoid closing down.
Sylvester Wambua, the head teacher at Kyanguli Memorial School, says the delay is threatening operations at the institution.
"The government is supposed to give us $95,861 - they have only given us $19,354.
"The free secondary education is really a challenge. We have creditors, we cannot pay them," Mr Wambua says.
Buckling under the weight of a $77,000 deficit this year, the school has been incurring debts to bridge the gap.
Mr Wambua is not the only school administrator grappling with a myriad of problems resulting from the lapse of support by the government.
Chacha Ngalando, the school administrator at Kithangaini Secondary School in Eastern Province is also struggling to make ends meet.
"There has been an increase in the student population, which means increasing the infrastructure. So where do you get the beds, the books with the peanuts that the government sends?" Mr Ngalando asks.
But the government has blamed the delay on school administrators, who it says have not provided proper bank accounts for the funds to be deposited.
And it promises that things will get better.
Education Assistant Minister Calist Mwatela says the programme needs time to succeed.
"It should be understood that our system is a transformation... It has its own challenges," Mr Mwatela says.
But the government has also admitted that it is facing a cash crunch.
Kenya's economy took a hit from the post-election violence witnessed early this year.
The government is also facing increased expenditure to meet the costs of a 42-member cabinet formed as part of a power-sharing agreement.
The cabinet will cost the government an extra $300m, and the ministry of finance warns it may be forced to shift funding from vital programmes.
Key ministries - among them medical services, roads, education and finance - have already had their budgets slashed to accommodate the increased government expenditure.
The free secondary school education programme may just be one of the casualties.
To cope with the funding crisis, administrators at schools serving the middle class have defied the government's directive not to charge fees.
Some schools are now asking parents to pay as much as $1,300 per year instead of the recommended $300.
If the government continues to delay the funding, the quality of high school education in public schools could be seriously compromised.
If this happens, it is the students from poor families who will pay a heavy price, as their parents cannot afford to take them to the costly private schools.
But the government insists that the programme has been a success.
President Kibaki says enrolment in secondary schools has shot up by 300,000 since January.
After a rocky start and with mounting challenges, the government faces an uphill task in providing high quality free secondary education.
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