A total of 920,765 out 1,035,664 students have taken up their slots in secondary schools, Education Cabinet Secretary Amina Mohamed has said.
Ms Mohamed said the number represents 90 percent turnout and vowed that the ministry will do everything possible for all candidates report to school.
Nyeri County has the highest number of students who have reported and is followed by Siaya, Bomet, Nyandarua, Kajiado, Muranga, Vihiga, Kisumu and Homa Bay.
Taita Taveta, Kilifi, Nairobi, Mombasa, Lamu, Kwale, Tana River and Isiolo have the lowest turnout.
"This low enrolment rate is unacceptable at this point in the transition process. These 'special' counties will therefore be the Ministry's point of first intensive focus," said Ms Mohamed.
Teachers Service Commission (TSC) Chief Executive officer Nancy Macharia directed headteachers to ensure that all pupils who wrote the Kenya Certificate of Primary Education examinations in 2018 join secondary schools.
"You are hereby asked to ensure that all pupils who sat for the 2018 KCPE examinations transit either to high schools or to vocational training colleges for the attainment of the 100 percent transition policy," Mrs Macharia told headteachers in a circular dated February 8.
She asked the headteachers to liaise with officials from the Ministry of Education and the provincial administration in their areas of jurisdiction for a successful exercise.
Deputy President William Ruto on Sunday asked all leaders to support the government in attaining 100 percent transition from primary to secondary schools.
Dr Ruto said there should be no excuse for any child's inability to access education and asked Members of Parliament to assist the less fortunate through Constituency Development Funds.
"We want to see every child go to school because it is their constitutional right," said Dr Ruto.
He spoke during a prayer service at the Pentecostal Evangelistic Fellowship of Africa church in South B, Nairobi.