Police used tear gas and batons to disperse protesters calling for sacking of Independent Electoral and Boundaries Commission (IEBC) officials before the re-run of a contested presidential vote later this month.
Hundreds of opposition protesters in Nairobi, Kisumu and Mombasa demonstrated near IEBC offices, disrupting businesses on nearby streets already suffering from reduced orders.
Opposition leader Raila Odinga is pushing for widespread IEBC reforms including the sacking of its chief executive Ezra Chiloba.
Mr Odinga says he will not participate in the October 26 election unless the demands are met.
In Nairobi, police fired tear gas canisters whenever protesters gathered.
In Mombasa, hundreds of opposition supporters gathered peacefully and were not confronted by police.
In the opposition stronghold of Kisumu, demonstrators erected barricades and burned tyres before police dispersed them.
Supreme Court judges, in annuling the August 8 polls, ruled that the election was “neither transparent nor verifiable”.
The prolonged election period has slowed economic growth with the government lowering its forecast to 5.5 per cent due to political uncertainty.