Voting did not take off in the morning in some parts of Nyanza as election officials failed to turn up for work over security and safety fears.
In some areas, officials could not distribute materials as youths blocked roads to prevent the election from taking place.
Voters also kept off polling centres in other areas.
Homa Bay County Returning Officer Michael Kosgey told journalists that the poll had failed to kick off in the morning as officials failed to report to work.
“The poll isn’t taking place because the officials we hired to oversee it have given it a wide berth in fear of their lives,” he said.
There were no polling officials or election materials in any of the Homa Bay County polling stations by 10am on Thursday.
National Super Alliance (Nasa) supporters blocked roads and disrupted the transportation of election materials to some polling centres.
Youths in Homa Bay town were moving from one polling station to another, checking if anyone was voting.
They also lit bonfires in the streets of Homa Bay town.
There was a heavy presence of security officials and anti-riot police engaged the protesters in running battles.
Police fired in the air and used teargas to disperse the demonstrators.
The election failed to kick off in most parts of Nyando Constituency, with most polling stations remaining closed.
At Ahero Multi-Purpose Hall, 14 deputy presiding officers had not left the tallying centre since Wednesday night for fear of victimisation.
Some 497 clerks were supposed to officiate the poll in the constituency.
Returning officer Carol Okky said only two field officers had turned up to pick the ballot boxes.
“We trained a number of poll officials but most of them disappeared for fear of their lives,” said Ms Okky.
However, she said, if the election takes place during the day, the time lost will be compensated.
Nyando Constituency has 148 polling stations and 74,640 registered voters.
In Vihiga County, Nasa principal Musalia Mudavadi’s home turf, voters did not turn up in the morning.
Most polling stations in the county opened at 6am but election officials remained idle.
There were no long queues as was witnessed during the August 8 General Election.
More than an hour after polling stations opened, no one had voted at Mululu polling station where Mr Mudavadi is a registered voter.
However, former Vihiga Governor Moses Akaranga cast his vote at Munugi Primary School in Sabatia Constituency, one of the few people to do so.
Mr Akaranga is the Jubilee point man in the constituency.
In Kisii County, voting started with no hitches but fewer voters had turned up in the morning than in the August 8 election.
A spot check by the Nation revealed no more than 10 voters in the queues in the early morning hours.
In August, as early as 5am, hundreds of residents were on the queues.
Mr Danvas Ongwacho, the presiding officer in Kisii Primary School polling station, said a few people had turned up to vote.
“We are however optimistic that the number will increase during the course of the day,” he said.
In Gusii municipal polling centre that has four stations, 14 out of the total 668 registered voters had cast their vote by 6.50am in one station.
Station 4 presiding officer Alex Mogire said the exercise was going on smoothly and peacefully and the KIEMS kits were in in perfect working condition.
The KIEMS kits had a slight hitch at one of the polling stations in Jogoo Primary School.
Presiding Officer James Osoro said the kit stopped working shortly after the station opened at 6.30am.
Voters had to wait for close to 30 minutes for voting to resume.
“We expect no more disruptions in the process … the kit problem has already been fixed,” he said.
By 7am, only six out of the 559 registered voters had cast their ballots in the station.
Voting in 111 polling stations in South Mugirango Constituency was delayed due to heavy rain and bad roads.
County Returning Officer Wilson Kimtai said voting in Nyandiwa, Nyamarambe and Bomanyama primary schools and Nyamarambe Hall was progressing smoothly though few voters turned up.
He said some KIEMS kits in some polling stations in Bogetenga Ward had a slight hitch but they started working an hour later.
In Kisumu County, election materials had not been dispatched to polling stations in Kisumu East and West constituencies.
Kisumu East Returning Officer Yvonne Okeyo said presiding officers have received death threats and she was unable to deploy them to polling centres.
Kisumu West Returning Officer Dennis Obara said nothing was going on in the entire Constituency.
“We are just seated here. We have been unable to transport the voting materials and even people are not turning up,” he said.
In Nyakach constituency polling centres were blocked by some residents as other stayed for fear of violence.
The gate to Kogallo Primary School polling centre was locked and access roads barricaded using boulders.
There were also no activities at Moro, Kabete and Burkamwana primary schools polling centres.
The constituency tallying centre at Thurdibuoro was also deserted.
Report by Barack Oduor, Derrick Luvega, Elgar Machuka, Elizabeth Ojina, Jadson Manduku and Victor Raballa
Opposition leader Raila Odinga has boycotted the poll and urged his supporters to stay at home.