About 1,300 Form One students failed to report to national schools where they were offered places, according to an Education ministry audit.
Only 14,934 students — 7,361 girls and 7,573 boys — made it to the 78 national schools countrywide.
Some 16,125 students who wrote the KCPE exam last year had been admitted to the top schools.
On Tuesday, the ministry will receive another report from principals showing the slots that have not been taken up and replacements made.
Schools close on April 12.
“So far, 93 per cent of students admitted to national schools had reported by last month,” former Education minister Mutula Kilonzo said.
“The remaining 1,291 slots were taken by students who reported late and through replacement coordinated at the ministry headquarters,” Mr Kilonzo said in the report on Form One returns (2013).
Tuesday’s report will show the number of students who reported to national special schools, extra-county, county, district and private schools.
The majority of students —389,299 — were expected to join district schools while county schools took 126,167, extra-county (36,115), special national schools (600) and 59,705 went to private schools.
There are 7,425 secondary schools in the country that absorbed 628,051 of the 819,295 pupils who sat their KCPE exam last year, meaning nearly 200,000 could not find places.
Mr Kilonzo said admissions for extra-county and county schools were still on last month following delays in Form One selections after exam results were delayed by three weeks.
“Replacements for these were done on March 14 at county level. Replacement for district schools was conducted on March 18,” he said.
Mr Kilonzo said admission letters were free and parents should not be cheated into parting with “presents, tokens of appreciation or inducements” to get the letters.
He asked MPs to assist students in their constituencies through Constituency Development Fund and bursaries.
At the same time, education lobby group, Elimu Yetu Coalition, has urged the government to streamline secondary school fees.
“The fees are prohibitive to children from poor families. Why should two schools of the same category have a difference of more than Sh20,0000 in fees?” Elimu coordinator Janet Muthoni-Ouko asked.