At least three opposition protesters died from gunshot wounds on Thursday during clashes amid Kenya's contentious rerun of a presidential election annulled by the country's top court in September.

Minutes before polls closed, Kenya's electoral chief Wafula Chebukati said voting in four counties will be postponed until Saturday due to violence, including Kisumu, Homa Bay, Migori and Siaya.

Read more: In Kenya, politics split on ethnic divide

Police clashed with protesters in several opposition strongholds, including Nairobi, Mombasa and Kisumu, where demonstrators reportedly set fires, blocked roads and thrown stones. However, national police chief Joseph Boinnet told reporters that security forces' actions did not amount to a crackdown.

"We don't use excessive force. In every situation we respond to the breakdown of law and order, our response has always been proportionate and measured," Boinnet said.

'Sham election'

Turnout appeared significantly lower compared to August's election, which witnessed nearly 80 percent turnout, according to local media.

"We should be seeing a very huge crowd lining up to vote, but on the contrary, today the polling station isn't very busy," a polling agent told DW in Nairobi.

Read more: 'My withdrawal not to blame for confusion,' Odinga tells DW

Although all the names of the candidates from the August vote remain on the ballot papers, the main opposition challenger, Raila Odinga has called for a "national resistance movement" to boycott the election.

"Do not participate in any way in the sham election," Odinga told a rally in central Nairobi. "Convince your friends, neighbors and everyone else not to participate." He called for a rerun election governed by a new, reformed electoral commission within 90 days.

Fears of violence

In Nairobi, one voter told DW: "It is my right and my duty to vote for the security of this nation." Despite the opposition's boycott, some of Kenyatta's supporters braved the polling stations to cast their vote.

After casting his vote, Kenyatta said the country needed to separate ethnic loyalties from politics in order for the country to move forward.

"What we have is a problem of tribalism, and tribalism is an issue that we must continue to deal with and fight with as we continue to develop our country," Kenyatta said. "We cannot achieve our goals if we continue to embark on tribalistic policies."

Read more: Kenya election: From 'fair and peaceful to democratic crisis

Security was tight going into the election after 37 people had died in violence after the August vote, with most of the victims shot dead by police.

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.

The uncertainty in Kenyan political life increases the risk of violence, according to Pat Thaker, regional director of Middle East and Africa for the London-based Economist Intelligence Unit.

"It's getting harder to see how Kenya can return to normality or 'business-as-usual' for the remainder of this year – and even into next year. The uncertainty in the political environment is set to continue at least for the rest of this year, and potentially increases the risk of violence, like we've seen after the 2007 election," Thaker said.

"Kenyatta is almost certain to win the second round almost uncontested, which in turn will probably trigger further brinkmanship in the form of another legal position from the opposition. What you're going to see is a lot of activity through the courts."

Democracy 'under siege'

In announcing its decision to annul the August 8 vote, the Supreme Court cited unconstitutional procedures and electoral systems that had been "infiltrated and compromised."

The court did not detail what remedial measures should be put in place but ordered the electoral commission to conduct a new vote within 60 days.

Read more: Opinion: Kenya needs statesmanship, not brinkmanship

It was the first time an incumbent African president's re-election had been blocked. Kenyatta responded to the court's decision by calling the justices "crooks."

Last week, Roselyn Akombe, a senior member of the electoral commission, resigned and went to New York. She claimed the electoral commission was "under siege" and that it could not guarantee a credible election.

ls/ng (Reuters, AFP, AP, dpa)