A total of 8.7 million learners have been registered under the newly introduced computer data system National Education Management Information System (NEMIS) as the government races against time to have 11.5 million enlisted by next month.
The registered learners are in public primary and secondary schools across the country and Nairobi county leads in the registration with 512,748 while Wajir has least registered students at 10,694.
The government is targeting to eliminate ghost learners, whose fees it may have been paying over the years.
On Friday, President Uhuru Kenyatta said the government would only provide capitation, books and medical cover to learners that are registered.
Public schools have now less than two weeks to register close to 3 million students raising concerns over huge number of possible ghost students.
Private schools have registered 1.82 million students.
President Kenyatta said the registration exercise should be concluded and asked headteachers and principals of schools to cooperate with the government in having accurate data.
"We need accurate enrolment data and this will be addressed by NEMIS. Its already becoming a great success. We must know how many students we have in schools across the country," said President Kenyatta at State House Nairobi during the 2018 Kenya National Drama Festival State Concert.
He said the new system which started in February will ensure that money allocated to schools benefits students and not some individuals.
"We want to know how many children we have in schools so that when we buy books we know whom we are buying for and the medical cover that we are rolling out in May is actually going to the benefits of students," added Mr Kenyatta.
Ministry of Education data indicate that there are 8.88 million pupils in primary schools secondary schools has 2.6 million.
For primary schools, the government pays Sh1,420 per child per year while in secondary schools, it pays Sh22,244 per child.
Which means more than the government may have been paying 5.6billion for ghost pupils in free primary education which was started in 2003.
The Ministry has indicated that going forward, cash disbursements for the Free Primary Education Programme, Free Day Secondary Education Programme and the KCPE and KCSE Examinations Registration Fee payments for candidates will be based on the NEMIS platform.
The government provides Sh14billion for free primary education and Sh32billion for free secondary education.
However, with 100 per cent transition to secondary schools, the government has since increased capitation to secondary schools.
The system was launched on January 27 this year to register all learners in primary and secondary schools.
At the same time, policy that requires head teachers not to work in their home areas may be reviewed, the Teachers Service Commission has said.
Chief Executive Officer Nancy Macharia told National Assembly's Education Committee that the policy had witnessed some teething problems since its inception last year.
"It is a good policy that we started to enhance national cohesion. We have received positive feedback and also concerns and we will look at them and see where to improve," Mrs Macharia told the Committee this week.
In 2016, in the 2017-2021 collective bargaining agreement, TSC and Kenya Union of Post Primary Education Teachers (Kuppet) and Kenya National Union of Teachers (Knut) agreed and signed that "in undertaking deployment the commission shall endeavour to delocalize the administration of the public institution.
Members of the Committee asked TSC to rein in officers who are promoting teachers in counties based on their ethic affiliation saying it should not be encouraged at all.
Mrs Macharia asked MPs to share with her specific cases where headteachers have been promoted without following merit in order to take appropriate actions.
"We have to deal with specific issues and I will be ready to receive report of specific incidents for appropriate action," said Mrs Macharia.