Jubilee supporters in Embu reportedly stoned anti-IEBC demonstrators and roughed up ODM county chair Moses Wamuuru on Monday.
The protestors were forced to flee on motorbikes after their demonstrations were disrupted by stone-throwing youths.
Their placards and banners were also torn and burnt during the counter-protests.
Wamuuru was accompanied by NASA supporters who were marching to IEBC offices near Agrican Church to present a memorandum.
The Opposition supporters are calling for the removal of IEBC CEO Ezra Chiloba and several other senior officers before the October 26 repeat polls.
But before they reached the premises, Jubilee supporters stopped the procession saying Embu is a Jubilee zone.
Anti-riot police quelled the situation, but Wamuuru condemned the actions and expressed disappointment.
Jubilee supporters burn posters and placards belonging to anti-IEBC demonstrators in Embu town, October 2, 2017. /REUBEN GITHENJI
"The action by Jubilee supporters is a violation of freedom to picket, which is provided for in the constitution. Embu leaders should cultivate political tolerance from rivals," the ODM county chair said.
He said he will lead demonstrations on Friday and include more Opposition supporters from all over the country.
NASA has called on supporters to demonstrate on Mondays and Fridays until IEBC gives in to their demands ahead of the repeat presidential election.
Coalition leader Raila Odinga skipped protests in Nairobi as police fired tear gas on protestors in the city.
In Kisumu, police also shot in the air to disperse hundreds of protesters who carried twigs and banners with the message "Chiloba Must Go".