Voters in at least 300 polling centres will be allowed to vote beyond 5pm following delays occasioned by logistical challenges.
The polling centres consist of entire Ndia and Nakuru East constituencies, which did not receive ballot papers on time following a mix-up in the distribution of the electoral materials.
The law provides that voting closes at 5pm.
Ndia Constituency has 70 polling centres while Nakuru East has 185.
According to IEBC Chairman Wafula Chebukati, ballot papers for Ndia ended up in Nakuru East and vice versa.
“We airlifted the papers to the correct polling station. Voting is going on as we speak,” Mr Chebukati said.
Three polling stations in Laikipia North Constituency were hit by insecurity, delaying the opening of polls, IEBC said without being specific on the incidents.
However, Mr Chebukati said security forces had restored calm in the area and polling had resumed.
In Turkana County, 18 polling stations did not open on time following a heavy downpour that pounded the area on Monday night.
Four polling stations each were affected In Turkana North and Turkana Central, eight in Loima Constituency and two in Turkana West.
“We wish to assure you all that for the polling stations that opened late we will compensate the time by extending the voting period by the same amount of hours that were lost before opening,” said Mr Chebukati.
IEBC also announced that by 2pm, some 40 per cent of voters in 25,000 polling stations had cast their ballots translating roughly to some seven million Kenyans who had voted by that time taking into account that each polling station has a maximum of 700 registered voters.
The total number of registered voters in the country stands at 19.6 million.
“We have been trying to monitor the turnout through KIEMS. The 40 per cent is based on data from 25,000 kits reporting as at 2pm. We expect the number to increase. This is the provisional figure but the actual turnout will be indicated in the forms submitted from the polling centres,” IEBC CEO Ezra Chiloba said.