Police were forced to fire in the air to disperse angry youths burning ballot papers at the Bungoma Primary School polling station in Nanyuki.
The angry voters engaged police in running battles as they complained that some aspirants names were missing from the ballot papers.
Voters at the Kanyoni nursery school also burnt the ballots saying the Jubilee party should be well organised.
This made the police to fire at them to disperse them.
Some of the voters also protested delays and hitches during the process.
The nominations failed to kick off on time in many polling stations but JP Secretary general Raphael Tuju said they will proceed as per the party's schedule.
Supporters, who started streaming in the polling centres from as early as 3am complained of delays.
Others opted to go back home.
A spot check by the Star revealed that voters had queued from 3 am but ballot papers were yet to reach the polling stations by 8am.
On Thursday, Uhuru warned against violence in the Jubilee Party primaries and ordered police to deal firmly with culprits.
He said the party will not entertain such chaos and that "any acts of violence will lead to disqualification".
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