The Education ministry has cancelled the KCSE results of 5,101 students and reported a 70 per cent rise in the number of cases of irregularities.
2,975 cases of cheating were recorded in 2014.
"We had an unprecedented rise of exam irregularities in 2015. I apologise to the public for them," Matiang'i
said on Thursday when the results were released.
"I will ensure it will not happen again. Let us all be responsible," he added, and commended Isiolo county for not having any cases of cheating.
He said Nairobi, Makueni and Meru counties were the most affected of the 47 counties.
The CS said the ministry will deal with candidates who cheated individually, through its secretariat.
"The secretariat that has been set up will address all queries regarding exam irregularities because our aim is to eliminate them," he said.
"Our children cannot work hard only for [their effort] to be rendered useless on account of irregularities. Let us all get together and ensure a credible examination system."
Matiang'i noted that a third of those who sat the exam have qualified for university. He said this was a 31.52 per cent improvement from 2014.
But Kenya National Union of Teachers secretary general Wilson Sossion said children should be given clemency, not punished, for cheating.
"Cases of cheating should be reviewed. We must not punish the students, for cheating is a societal problem that needs to be addressed. Punish the actual culprits," he said.
Sossion noted that the cheating did not result from the teachers' strike over a basic salary increment.
But he said: "The curriculum was affected by the eight-week strike; that was a long period. We asked the minister to reschedule the exam."
He said officials will ensure there are no irregularities in the 2016 exam.
The Senate Committee on Education said it was concerned about the results given the irregularities reported.
A total of 525,802 students sat the KCSE exam in 2015 compared to 485,547 in 2014. They can send their index numbers to 22252 for their results.