Seventy six registered candidates from South Sudan did not write KCSE tests in Turkana due to insecurity concerns.
County education director Pius Ong'oma noted tension after killings at Lokichogio Mixed Secondary School caused the students from the neighbouring country not to turn up.
A fresh concern is now that the absence of the South Sudan nationals will affect the county's overall performance.
Toney Ewoton, county secretary of the Kenya National Union of Teachers, said on Mibdat that the Ministry of Education should not consider the absence of the 76.
"This should be done so Turkana's mean score is not affected," he told journalists in his office.
Ewoton also asked Kenya National Examination Council to address the issue of examination centres.
Heavy rainfall in parts of Turkana caused students from about seven schools to gather at one centre.
"Students are not used to that kind of environment," the secretary said, adding KNEC should ensure students write the examinations in their classrooms next year.