There was anxiety and panic after a number of the KCPE papers mysteriously disappeared.
The papers from Gatundu North Constituency in Kiambu County mysteriously disappeared prompting security officials to action.
Already, officials in charge if the KCPE exams in Gatundu North are under probe over the matter.
According to The Star, the officials have swiftly been replaced with others at the end of Wednesday's exams.
The matter has brought the spotlight on the integrity and transparency of the national exams.
The incident comes hours after President-elect Uhuru Kenyatta assured the country that the entire examination process would be conducted above board.
The President on Wednesday was on hand at the Westlands Primary School to witness first hand to ensure the integrity and transparency of the process before the candidates sat for their KCPE 2017 Science Paper.
He was accompanied by top education officials led by Cabinet Secretary Fred Matiangi.
Matiangi on Monday announced the introduction of a three-level security management system to curb any irregularities.
The government at the same time promised Kenyans that it will ensure the current political tension and violence witnessed in some parts of the country will not disrupt the national exam.
Several senior government officials among them cabinet secretaries have been on hand to open of seals of the examination papers in various parts of the country as a show of confidence.
The government on Tuesday announced they had acquired 20 modern scanning machines expected to improve speed and accuracy when processing the examinations.
A total of 1,003,556 candidates will sit for this year's KCPE across 28,566 examination centres across the country.