A total of 2,543 candidates who registered for the KCPE exam did not sit the test, KNEC CEO Mercy Karogo said on Thursday during release of results.
A total of 1,181,725 registered for the exam but 1,179,182 sat the paper.
A total of 28,467 exam centres were used.
The KCPE exams were delayed as a result of Covid-19 pandemic.
The 2020 KCPE exam started on March 22 and ended on March 24, with rehearsals having been done on March 19.
Last year, 1,083,456 learners sat the 2019 exam.
Among 3,500 girls in primary school who were found to be pregnant, more than 200 candidates sat for the exam.
Education CS George Magoha spoke of the trials of reopening schools amid a pandemic.
"There were those who castigated the move, saying we were putting the lives of children at risk and making them guinea pigs....we stood firm," he said.
Seven candidates were found with prepared notes in exam rooms.
Magoha said all results will be released, but culprits will be pursued.
Meanwhile, TSC CEO Nancy Macharia said all teachers can now access the vaccine.
This is after a ministry meeting with President Uhuru Kenyatta, who approved the move.
Initially, it was teachers above the age of 50 who were prioritised during the first phase of vaccination.
Macharia urged all tutors to take advantage of the new directive to get the jab as schools are set to open in May.
Macharia announced that at least 15 primary school teachers have died since the Covid-19 pandemic struck the country in March 2020.
"We have lost three deputy head teachers and eight head teachers to the pandemic," she said.
Macharia said going forward, the commission has come up with measures to protect all teachers from the virus.
"First we instructed our medical health insurance provider to cover all teachers against Covid-related ailments which they have since complied with," Macharia said.
