Private schools performed better than public ones in the 2015 KCPE exam, whose results were released on Wednesday.
The mean score for public schools dropped from 187.58 the previous year to 180.87, Education CS Fred Matiang'i said in the announcement.
"This is very worrying," Matiang'i said at Mtihani House in Nairobi, noting the score for private schools improved from 229.94 in 2014 to 230.14.
This brings to the fore the teachers' strike over a 50 to 60 per cent basic salary increment that began in September and lasted five weeks. Private schools were not affected by the strike.
Teachers posted to Northeastern refused to return to work after an al Shabaab bus attack in November 2014 that left 28 of their colleagues dead.
Several other attacks by the terror group in the area resulted in the mass exodus of other public workers as well.
Regarding gender balance in student registration, Matiang'i reported that 49.6 per cent girls and 50.4 per cent boys were enrolled.
He added: "Twenty three counties registered more girls than boys in 2015 but we must work on the gap in counties such as Turkana, Garissa, Mandera and Samburu so we do not cancel out achievements at the national level."
He said cheating was registered at 11 of the 25,127 exam centres.