The election commission said the poll in Beni, Butembo and the western town of Yumbi would be delayed until March because of insecurity and an Ebola outbreak in the east, which has so far claimed more than 300 lives.
In the eastern city of Goma, police fired tear gas during a standoff with protesters and demonstrators in Butembo barricaded streets and set fires at crossroads, according to local police. Those include tons of hand sanitizer - Ebola is spread via infected bodily fluids - and the screening of all voters entering polling stations.
Explaining the three exclusions, it said on Wednesday: "Elections lead to important movements of voters toward polling places, thus ... raising the risk of propagation of this disease (Ebola) and providing the conditions for terrorist attacks".
Opposition supporters suspect Mr Kabila is trying to cling on to power.
Ambulances drive into an attacked ebola treatment center during protest by demonstrators over their exclusion from the presidential election in Beni, Democratic Republic of the Congo.
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Some protesters carried crosses with the words "RIP Kabila" and saying that departing President Joseph Kabila's preferred successor Emmanuel Ramazani Shadary "will never be our president".
Beni's civil society urged residents to turn out en masse on Sunday.
Seventeen of the 24 who escaped subsequently tested negative for Ebola while seven have not yet been screened, a health ministry spokesperson told Reuters. Protesters also attacked the office of the government agency coordinating the Ebola response before United Nations peacekeepers pushed them back, Abedi said.
The epidemic in a volatile part of DRC is now surpassed only by the 2013-16 outbreak in West Africa, where more than 28,000 cases were confirmed.
The uproar over the voting delay has "badly disturbed" Ebola response work in Beni and Butembo, Congo's health ministry said.
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In general, communities in Ebola-affected areas have supported the response, he said. "These people deserve to have their say as well". And in a separate report detailing the latest outbreak trends, the World Health Organization said cases continue across a geographically dispersed area, and although Ebola infection numbers continue to decline in Beni, the outbreak is intensifying in Butembo and Katwa, with new clusters popping up elsewhere.
Leader of the delegation Joseph Malanji who is also Zambia's Foreign Affairs Minister told the BBC he was unable to judge whether the election will be free and fair.
"The holding of inclusive, transparent, credible and peaceful elections will be important for the EU's future engagement with the democratically elected authorities in the DRC for the future development of the country in the interest of the Congolese people", added Mogherini.
He dismissed opposition allegations that campaigns had faced restrictions, including blocked flights and supporters assaulted.
The three cities, home to more than 1.2 million of Congo's roughly 40 million registered voters, are known as bastions of opposition to Kabila. He called on all Congolese to remain calm and vote without violence.
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