Some 1.3 million learners returned home last week after enduring ten weeks of confusion.
Interviews with learners, teachers, parents and other education stakeholders paint a picture of many hiccups in the ambitious attempt by the government to transition learners from 8-4-4 to the new 2-6-6-3 system.
Teacher shortage, delayed disbursement of capitation and inadequate learning facilities still dominated the list of challenges cited by teachers, parents and children as first term came to a close.
Slow distribution of textbooks occasioned by delayed disbursement of capitation money also hampered the smooth transition in many schools.
It has also emerged that a number of Grade Six students may have chosen to enroll in Class Eight to escape the confusion in JSS, a matter that insiders say may cripple the smooth transition to JSS.
What is further shocking is the revelation that some 25,000 students who were expected to report to the various Grade Seven classes in public or private schools still remain unaccounted for.
Appearing before the Senate Education Committee, Education Cabinet Secretary Ezekiel Machogu revealed that the government could not account for these students several weeks after schools opened.
"We expected a 100 per cent transition of 1,253,577 from Grade Six to Grade Seven. I'm happy to inform Kenyans that for Junior Secondary Schools, we are at 1,228,506 translating to 98 per cent,'' Mr Machogu said.
The JSS challenges also caught the attention of MPs with the Parliamentary Select Committee on Education raising concerns over transition.
Primary school head teachers, who also double as principals of the JSS, mentioned delayed funding as one of the major challenges that disrupted the transition.
Through their national chairman Johnson Nzioka, the heads said schools experienced cash crunch the entire term as the Sh9.6 billion was released just a week to the schools' closure.
''The challenge we faced in the term was capitation in schools. The government promised us the money in January but it seems it took a long route to arrive at the school's account,'' Mr Nzioka said. He disclosed that some schools missed the funds.
Mr Nzioka blamed the State for delayed disbursement of the funds which he said, forced many heads to resort to borrowing to run schools.
''Heads have to decide if it's paying debts, planning for the labs which should be given priority, or securing the equipment. I don't think classrooms are a priority as of now,'' he stated. Nzioka said although the government distributed text books, not all learning areas were covered.
Parents however argued that inadequate classrooms weighed down the transition progress.
Through their association chairman Silas Obuhatsa, parents said it was easier to construct classes in secondary schools than to put up laboratories in each primary school.
''Building more classrooms in secondary schools which already have laboratories would be easier and more cost-effective than trying to create new labs in primary schools,'' Mr Obuhatsa said.
While in the Senate, CS Machogu admitted to the shortage of infrastructure saying it will take a year for this to be in place.
''As of now what we are doing as a priority is to build laboratories. The government has allocated Sh4.5 billion towards the construction of laboratories in junior secondary schools,'' he said.
In the confusion, some heads took advantage to push additional levies on parents.
Some schools charged money for desks, meals and other levies not sanctioned by the ministry, sparking an outcry on cost of JSS.
Basic Education PS Belio Kipsang cautioned school heads against charging illegal levies and even threatened action on offenders. Dr Kipsang argued that the government had catered for learner's education.
However, by close of the term, no action had been taken on any teacher despite the complaints.
A teachers union argued that delayed funding had pushed head teachers to introduce illegal levies to ensure learning in schools.
''How do you expect head teachers to run schools without funds, classes and books? This is the reason why they are charging parent levies,'' said Kenya Union of Post Primary Education Teachers Secretary General Akelo Misori.
