Voting failed to take place in four Nyanza counties, while low turn out characterised the event in others and also in western Kenya.
There was no ballot cast in Kisumu, Siaya, Homa Bay counties and parts of Migori County after polling clerks refused to show up for work, citing threats on their lives.
Although the election went on smoothly in Kuria East and West of Migori County, Independent Electoral and Boundaries Commission (IEBC) later said it was among the counties where voting will be repeated on Saturday.
In Kisumu, where rioters fought the police and targeted polling centres, material for voting remained in the stores after presiding officers failed to pick them for fear of being victimised.
No ballot materials reached the 140 polling stations in the constituency.
Presiding officers who were to pick the materials at the Kisumu East sub-county offices called the returning officer to inform her that they were unable to do so.
“We are now grounded because we can’t risk their lives,” the RO, Ms Yvonne Okeyo, said.
In Kisumu West, polling materials were similarly not dispatched to polling stations.
Returning Officer Dennis Obara said nothing went on in the entire constituency as service providers, who had been sought to transport election materials, kept off after they were threatened not to do so.
Kisumu Central Constituency returning officer John Ngutahi said out of the 399 officers, only four reported for duty.
Voting across polling centres in nine constituencies in Kisii County was marred by voter apathy, with many residents giving polling stations a wide berth.
Kisii Governor James Ongwae, Senator Sam Ongeri and Woman Rep Janet Ong’era all honoured the pledge that they would not vote, made during opposition leader Raila Odinga’s visit to the county on Monday.
Presiding officer Vincent Nyambane said that only 66 people had voted at the station by 1:30pm out of the overall 568 registered voters.
Nyaribari Masaba Constituency Returning Officer Mark Manco said most polling stations had recorded lows of about 11 per cent voter turnout by midday.
“Voting in a few of our polling stations started very late, like in Ibacho polling station where the first voter cast his vote shortly after 9am despite the station having opened at 6am,” Mr Manco said.
Elsewhere, after a relatively quiet morning, chaos and protests rocked several parts of Kakamega County in the afternoon, with police involved in running battles with hundreds of protesters.
This stand-off started at about midday when most of the protesters who were chanting anti-Jubilee slogans, barricaded the Kakamega-Kisumu highway using stones, twigs and broken bottles at the Ikambi wa Khayega market.
Police had a rough time controlling the rowdy youth, some of who used a swarm of bees they had carried in hives to block the entrance to Matsakha Primary School Polling Station in Malava Constituency, forcing would-be voters to keep off.
Earlier, a man in the area beat up his wife accusing her of going to vote against his wish.
“It is common knowledge that I am a Nasa supporter yet my wife sneaked to go and vote for Jubilee,” he told journalists.
Malava Constituency Returning Officer Isaac Ruto said there were isolated cases of Kiems kits hitches, which have since been addressed.
Area MP Malulu Injendi cast his ballot at Lugusi Primary School and was optimistic that Jubilee would garner more than the 8,000 votes it bagged on August 8.
In Mumias, voting in two polling stations in Mumias West Constituency, Kakamega County was disrupted by rowdy youth.
Ugana and Buyundo polling centres in Musanda Ward were closed after the youth stormed the schools and evicted the polling officials.
In Nambale, Busia County, a number of polling stations were forced to close as early as 1pm after chaos erupted, as many others witnessed low voter turnout.
At Mabunge Primary School, extra police officers were called in to back up their colleagues who had been overpowered by youths who stormed the centre and ran away with ballot boxes before burning them on the road just outside the school compound.
In Bomet, Governor Joyce Laboso, who was among voters who cast their ballots, censured Nasa presidential candidate Raila Odinga for refusing to participate in the repeat election, yet he was the one who moved to the Supreme Court to seek the nullification of the exercise.
Reports by Justus Ochieng’, Sylverster Mukele, Nelcon Odhiambo, David Kwalimwa, Linet Wafula, Derick Luvega, Benson Amadala, Magati Obebo, Geoffrey Rono, Vivere Nandiemo, Elgar Machuka.