Kenya is holding its second presidential election since August despite high tension and the main opposition leader's call for his followers to boycott.

Some polling stations in opposition areas did not open, while police fired tear gas in clashes with opposition supporters in Kibera, a Nairobi slum.

Voting, meanwhile, proceeded in areas where President Uhuru Kenyatta has support, but fewer voters were turning out in comparison to an August 8 election that the Supreme Court nullified because it found illegalities and irregularities in the election process.

Voters lined up before dawn at a polling station in Kenyatta's hometown of Gatundu and electoral workers prepared ballot papers by flashlight after heavy rains knocked out power to the site.

Downpours also disrupted the delivery of ballot papers in Kenya's Kitui area, according to local media.

Kenyatta, who was declared the winner in the August vote, said in a televised address on Wednesday that security forces would be deployed nationwide to ensure order, and he urged Kenyans to vote while respecting the rights of those who do not.

Opposition leader Raila Odinga said the new vote would not be credible because of a lack of electoral reform since the August election and accused Kenyatta of moving a country known for relative stability and openness toward authoritarian rule.

Odinga's call for an election boycott appeared to have resonated strongly in Kisumu, Kenya's third-largest city and an opposition stronghold.

Many polling stations were closed even after the official opening time of 6am and Kenyan media reported that opposition supporters had blocked roads leading to some polling stations in the region.

Odinga has urged followers to stay away from polling stations because of concerns about a crackdown by security forces.

Human rights groups said police killed dozens of people during protests after the August vote; authorities confirmed a smaller number of deaths and said they had to take action against rioters.

Odinga and Kenyatta, who seeks a second term, also faced off in a 2013 election marred by opposition allegations of vote-rigging.

The opposition leader also ran unsuccessfully in 2007 - ethnic-fuelled animosity after that vote killed more than 1,000 people and forced 600,000 from their homes.

Many observers say Kenya's ethnic-based politics overshadow the promise of its democracy. Kenyatta is a Kikuyu, while Odinga is a Luo.