The Ministry of Education has raised concern after more than 200,000 learners failed to appear for Grade 7 admission.
Learners in Grade 7 are the pioneer class of Junior secondary school under the Competency-Based Curriculum, CBC.
The learners are supposed to be in their third week of the Junior secondary following the onset of learning on January 30.
Education CS Ezekiel Machogu said the Ministry will investigate why the students have not been admitted.
"Through the multi-government approach together with our local leaders, we will find out where the learners are," Machogu said.
The CS was speaking at Kenya School of Tvet on Wednesday.
Some 1.2 million learners sat Grade 6 national assessment exam in November 2022 and their transition to Junior secondary was expected to be 100 per cent.
"So far we have between 900,000 - 1 million learners who have so far been admitted, according to the data we have," Machagu said.
It remains unclear whether the deficit has been created by learners who have transitioned to class 8, or if they have been enrolled to private schools.
On Monday, Basic Education PS Belio Kipsang revealed that some teachers and parents were colluding to enroll Grade 7 students for KCPE exams for purposes of ensuring they do not learn under the CBC system.
The PS said in a circular that this was being done through the falsification of school records, birth records and biodata for Grade 7 and attempts to change/obtain new birth certificates.
He added that other schools have gone a notch higher to generate a new UPI number for the Grade 7 learners.
"Facilitating transfers of Grade 7 into other schools and presenting them as Class 8 transfers," Kipsang said.
Primary schools have the last cohort of learners under the 8-4-4 system who are due to sit their Kenya Certificate of Primary Education exam at the end of the year.
Such falsified registration would mean Grade 7 learners will skip Junior secondary and instead revert to the old syllabus by joining the last cohort of Standard 8 learners.
Last week, Machogu said it's not possible to transfer the children because the unique NEMIS number cannot allow it.
He also faulted school heads for taking the children to another step without following due procedure.
"The NEMIS system will note any discrepancies when one student has skipped a step in their education," Machogu said.
Kipsang wrote the circular to regional and subcounty directors on education on February 8.