Kenyan police clashed with opposition supporters where burning barricades and gangs of youths prevented voting in some towns in an election re-run, seeking to challenge the credibility of President Uhuru Kenyatta's expected victory.

In the western city of Kisumu, stone-throwing youths heeding opposition leader Raila Odinga's call for a voter boycott were met by live rounds, tear gas and water cannon three hours after polling stations were meant to have opened. There were no immediate reports of casualties.

The election is being closely watched across East Africa, which relies on Kenya as a trade and logistics hub, and in the West where Nairobi is regarded as a bulwark against Islamist militancy in Somalia and civil conflict in South Sudan and Burundi.

By and large the security situation in the country is OK. Polling stations have been opened in over 90 per cent of the country and voting has commenced," Interior minister Fred Matiang'i told Citizen TV.

In the western town of Migori, another opposition stronghold, several hundred young men milled around on a main road littered with rubble and burning barricades, according to footage on the domestic NTV channel.

The handful of polling officials who pitched up to work in Kisumu, the scene of major ethnic violence after a disputed election in 2007, cowered behind closed doors, unable to distribute any voting material.

Such problems, already acknowledged by judges and the election commission, are likely to trigger legal challenges to the run-off and could stir longer-term instability in a country riven by deep ethnic divisions.

The re-run follows an August vote whose result - a Kenyatta victory - was annulled by the Supreme Court due to procedural irregularities.

Kenya elections rerun: in pictures Show all 20 1 /20 Kenya elections rerun: in pictures Kenya elections rerun: in pictures Kenya elections rerun A National Super Alliance protester yells as nearby police officers Getty Images Kenya elections rerun: in pictures Kenya elections rerun Residents some brandishing swords, throw stones towards Kenyan police officials AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun Supporters of National Super Alliance (NASA) presidential candidate Raila Odinga burn tires AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun A security officer checks a voter before letting him participate in a presidential election REUTERS Kenya elections rerun: in pictures Kenya elections rerun Smoke rises from tear gas fired by riot policemen to disperse supporters of Kenyan opposition leader Raila Odinga REUTERS Kenya elections rerun: in pictures Kenya elections rerun An opposition supporter gestures with a knife during clashes with police in Kibera slum REUTERS Kenya elections rerun: in pictures Kenya elections rerun Riot police fire tear gas to disperse supporters of Kenyan opposition leader Raila Odinga REUTERS Kenya elections rerun: in pictures Kenya elections rerun Residents throw stones towards Kenyan police officials AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun A protester prepares to throw back a teargas canister AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun A Kenyan woman prepares to cast her vote by gas lamp, just after dawn AP Kenya elections rerun: in pictures Kenya elections rerun Opposition supporters run away from police in Kibera slum during clashes in Nairobi REUTERS Kenya elections rerun: in pictures Kenya elections rerun Supporters of National Super Alliance presidential candidate Raila Odinga burn tires AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun People queue to cast their vote at a polling station REUTERS Kenya elections rerun: in pictures Kenya elections rerun Kenyan police officials react as teargas fills a street in Kibera AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun Members of the Kenyan Independent Electoral and Boundaries commission check ballot boxes AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun Kenyan police officers chase National Super Alliance protesters Getty Images Kenya elections rerun: in pictures Kenya elections rerun People cast their votes at a polling station REUTERS Kenya elections rerun: in pictures Kenya elections rerun Residents look on as Kenyan police officials walk towards a group of demonstrators AFP/Getty Images Kenya elections rerun: in pictures Kenya elections rerun A protester throws stones as riot police REUTERS Kenya elections rerun: in pictures Kenya elections rerun People queuing outside a polling station REUTERS

In Kisumu Central, constituency returning officer John Ngutai said no voting materials had been distributed and only three of his 400 staff had turned up for work. One nervous official described his work in the city as a "suicide mission".

"We don't have any options," Ngutai told Reuters as he and two presiding officers sorted thousands of ballot papers into piles, work that should have been completed the previous day.

Kisumu businessman Joshua Nyamori, 42, was one of the few voters brave enough to defy Odinga's stay-away call but said intimidation had put paid to his desire to cast his ballot.

"I know it's not a popular move," he said. "Residents fear reprisal from political gangs organised by politicians. This is wrong."

A decade after 1,200 people were killed over another disputed election, many Kenyans are ready for trouble although on the eve of the vote Odinga backed off previous calls for protests and urged supporters to stay out of the way of police.

"We advise Kenyans who value democracy and justice to hold vigils and prayers away from polling stations, or just stay at home," he said.

Odinga's National Super Alliance coalition, which has been accused of harrassing polling staff in the run-up to the vote, is likely to present a lack of open polling stations as proof the re-run, organised in less than 60 days, is bogus.

The head of the election commission said last week he could not guarantee a free and fair vote, citing interference from politicians and threats of violence against his colleagues. One election commissioner has quit and fled the country.

Kenyatta, the US-educated son of Kenya's founding father, has made clear he sees the vote as legitimate. In central Nairobi, where support for the two protagonists is more mixed, early turnout was significantly down on August.

Anti-riot police were patrolling in Kibera and Mathare, two volatile Nairobi slums. Nearly 50 people have been killed by security forces since the August vote.

In a statement issued by the U.S. embassy, foreign missions called for calm from all sides but acknowledged that the vote had been damaging to regional stability.

"Following this election, there must be immediate, sustained, open and transparent dialogue involving all Kenyans to resolve the deep divisions that the electoral process has exacerbated," it said.

Speaking on the eve of the vote, Kenyatta assured his countrymen and Kenya's allies that order would be restored.

"I tell all our international partners that we will get through this," he said. "We cannot remain in a perpetual state of politicking.