Grade 7 learners who will remain in primary schools, will still be under their school headteacher.
The concerns were raised by MPs when TSC faced the education committee on Monday.
TSC legal officer Cavin Anyuor said junior secondary school will still be under primary school management.
Kitutu Masaba MP Clive Gisairo had inquired how teachers will run the two categories separately.
“Who will be the administrator, will they have different management in the same school or how will that be done?” he said.
Anyuor responded saying Grade 7 will still be managed under primary schools.
“As it stands now the administrator will still remain the headteacher of that primary until junior secondary takes off,” he said.
Parents won big after President William Ruto scrapped the national examination that could have been used to determine the transition of Grade 6 learners to junior secondary school.
Ruto also ordered that learners who sat the Kenya Primary School Education Assessment proceed to junior secondary in the same primary school.
“The Grade 6 Kenya Primary School Education Assessment will not be used for placement in Junior Secondary School," the preliminary report brief issued by State House Spokesman Hussein Mohamed said.
"Instead, it will be used as an assessment to monitor learning progress and provide feedback to education sector players on areas that require intervention.”
The directions were issued in a preliminary report by the working party after they met President Ruto at State House on Thursday.