The audit, which assessed the financial books of the Basic Education Department, flagged Sh1.78 billion used for classroom construction as unaccounted for.
The ministry had initially reported spending Sh4.48 billion on the project , exceeding the approved budget of Sh2.69 billion by a significant margin.
The construction of classes aimed to address both congestion that already plagued the institutions and prepare for the anticipated transition of Grade 6 learners to junior secondary schools under the new CBC.
This was as before the decision to host Junior School was made.
''In the circumstances, the accuracy, completeness, validity and regularity of the expenditure amounting to Sh1,784,068,016 could not be confirmed as a proper charge to public funds,'' the auditor's report reads.
According to the report, the ministry failed to provide documentation on procurement procedures and contractor selection for the project.
Additionally, auditors identified a lack of market research to justify the set cost of Sh709,398 per classroom and missing status reports on construction progress.
However, while appearing before the Education Committee of the National Assembly, Basic Education Principal Secretary Belio Kipsang acknowledged discrepancies in funding. He said that the Treasury only provided a fraction of the Sh4 billion that was initially approved for construction of the classes.
He said the government provided Sh2.6 billion which was not enough for the construction while the balance was to be provided during the Supplementary Estimates two of Financial Year 2021/2022.
This, however, was never provided.
To cater for the shortfall , Kipsang explained that the Ministry of Education got funding for construction of the classes from other sources.
He said that the ministry pulled funds from the Secondary School Infrastructure Improvement funds amounting to Sh1.45 billion.
Additionally, the ministry reallocated Sh692 million originally budgeted for purchasing desks in primary schools to fund classroom construction, bringing the total allocation for the project to Sh4.14 billion.
"Therefore the total allocation of CBC classrooms was Sh4,141,800,000," Kipsang said.
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The report has also questioned procurement method used for the construction of the CBC classrooms and how the various contractors were identified.
The ministry, however, defended its actions, explaining that the construction was undertaken under the Kenya Economic Stimulus Package to revitalise the economy that was then struggling from the effects of Covid-19 pandemic.
Kipsang explained that at the sub-county level local contractors were identified within the vicinity of the benefiting schools.