Thousands of students who have not registered with the National Education Management Information System (Nemis) are denied medical treatment due to lack of National Hospital Insurance Fund (NHIF) number.
On Tuesday, principals complained that thousands of their students are being denied medical attention.
But the Education ministry stressed that all students must register with Nemis to get an NHIF number for treatment.
Speaking during the ongoing 44th Kenya Secondary Schools Heads Association (Kessha) annual national conference in Mombasa, the Director for Secondary Education, Mr Paul Kibet, said the ministry is having issues with students who are not fully registered in Nemis.
"For the students to be treated, they must be registered with NHIF. Go to your schools' Nemis accounts and you may not have captured the details of the parents. When the details of the parents or guardians are missing, NHIF will not issue a number," Mr Kibet said.
He added: "The systems works such that when we complete all our data, it populates the NHIF system and if the system (NHIF) misses the details of parents it will not issue an NHIF number. If something is missing, the student will be locked out of the scheme."
In April last year, President Uhuru Kenyatta launched the Sh4 billion medical cover scheme for secondary school students.
In a question-and-answer session, Mr Kibet said sometimes when students are taken to hospital, they cannot access treatment because some of their details are missing in Nemis.
"Because our system has what we call 'handshake' protocol with NHIF system, anytime a student's details are captured they are sent to NHIF to ensure they are given a personal NHIF number. If the details are not fully captured, the details are not complete," Mr Kibet said.
"Please go the whole way. Step one is the normal bio data. We want Nemis to grow so embrace it... In August, we want all schools to submit their form one projections," he said.
The ministry has expanded Nemis bandwidth to ensure principals have enough time to upload details and monitor the system, Mr Kibet added.