The low turnout of Kenya's election re-run dealt a blow to President Uhuru Kenyatta's hopes for a decisive second-term mandate. Picture: AP Photo/Ben Curtis

Nairobi - Results of Kenya's presidential election re-run started to trickle in on Friday, with early estimates of the turnout at below 35 percent, dealing a blow to President Uhuru Kenyatta's hopes for a decisive second-term mandate.

With nearly all followers of opposition leader Raila Odinga heeding the veteran's call for a boycott, Kenyatta's victory is not in question.

Less clear is his ability to unite the east African nation, whose deep ethnic divisions have been exposed during the bloody and controversial election process and multiple court cases in the past three months.

The first election, in August, was annulled by the courts because of procedural irregularities, denying Kenyatta a simple victory over his long-term political rival.

Voting on Thursday was marred by skirmishes between police and stone-throwing opposition supporters, who prevented polling stations from opening in four pro-Odinga counties, forcing election officials to postpone the exercise by 48 hours.

The election commission said more than one in 10 polling stations failed to open. Its chairperson, Wafula Chebukati, Tweeted overnight that 6.55 million ballots had been cast - just 34.5 percent of registered voters.

By contrast, turnout in the August election was 80 percent.

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

In the western city of Kisumu, police used tear gas and fired live rounds over the heads of stone-throwing youths. Gunfire killed one protester and wounded three, a nurse said.

In Homa Bay county next door, police said they shot dead one protester and injured another.

There were similar scenes in Kibera and Mathare, two volatile Nairobi slums. At least one person was shot in the leg, a Red Cross official said, and a church was fire-bombed.

Around 50 people have been killed, mostly by security forces, since the original August 8 vote, raising fears of sustained violence only a decade after 1 200 people were killed in serious ethnic fighting triggered by another disputed vote.

Legal challenges to the re-run are expected. If they fail to provide a clear path out of the crisis, including an order for another re-run, many Kenyans are fearing protracted political stalemate between the Kenyatta and Odinga camps.

"Unless the courts annul the election, Kenyatta will move forward without a clear mandate and Odinga will pursue a protest strategy whose chances of success in the circumstances are not very high," said International Crisis Group analyst Murithi Mutiga.