Lobby groups have urged the Education ministry to shelve the contentious Form One selection rules favouring pupils in public schools.
The selection method adopted for the first time last year, said the Kenya National Association of Parents (Knap) was "discriminatory" to hardworking pupils in private schools.
"Let us not punish parents who take their children to private schools," urged Knap secretary general Musau Ndunda.
At the same time, Kenya Private Schools Association chairman John Mwai said it was "immoral" to deny private school pupils a chance to join their dream schools.
"These pupils sat the same KCPE exam with those in public schools. It is immoral to deny them vacancies in the national schools," Mr Mwai said.
Some parents with pupils in private schools have expressed concern that the selection formula might deny their children dreams of joining top schools despite performing well.
"I am worried that my daughter may not get a place in her dream school, Alliance Girls, despite having scored 418 marks in KCPE," Mr Blaise Okinyi told the Nation.
His daughter Bettina Amondi emerged the top candidate in Narok County.
The ministry at the weekend stood its ground that the new Form One selection method would stay. (READ: Form 1 selection formula to stay)
Education secretary George Godia maintained the method would be used during the selection to national schools.
According to the new rules, for every three pupils admitted to national secondary schools, there will be only one from private schools.
"The idea here is to create equity and fairness when selecting the pupils to national schools as it is expounded in our Constitution," Prof Godia told the Nation.
This year, more pupils from private schools will be affected after 5,806 candidates scored 400 marks and above compared to last year's 2,723.
Last year, the Kenya Private Schools Association took the Education ministry to court protesting that the selection method was discriminatory.
But a three-judge bench ruled in favour of the ministry, saying the policy introduced last year was not in any way discriminative.
"If merits were the only qualification to be considered in Form One selection, it would mean private schools would take the large share in top schools," the judges observed.
Judges Jeanne Gacheche, George Dulu and Aggrey Muchelule said even though the quality of education in public schools was heavily compromised, it would be unfair to select Form One students based on merit alone.
Meanwhile, special needs teachers have called on the ministry to put physically challenged pupils in their own category in national examinations ranking.
Kenya Union of Special Needs Education Teachers secretary general James Torome said last year's KCPE ranking was unfair to physically challenged pupils.
"If the ministry ranks them in different categories according to their status, it will make it easy for those who are from poor backgrounds to secure sponsorship," Mr Torome said in Narok town on Monday.
He said the minister only considered visually impaired and physically handicapped students.
"There are other students who were not mentioned and are deaf, autistic have learning difficulties and multiple disabilities and end up living hopeless lives," he added.