Bienvenu Esimba, governor of DR Congo's northwestern Mongala province, said the clashes broke out Wednesday in the provincial capital Lisala when members of the sect burned dozens of houses and attacked a market before launching an assault on local electoral commission offices.
"The toll from the clashes is 14 militiamen from the political-religious cult and three dead police officers," Esimba told AFP by telephone, adding that cult leader Wami-Nene was among those killed.
DR Congo is mired in political crisis two days after Kabila's second and final term in office had been due to end on December 20, with no indications that he is planning to step down.
Esimba said the cult members, armed with AK-47 assault rifles, had burned 47 houses and attacked the offices of the electoral commission because they judged the institution to be "useless".
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Troops had to step in to "neutralise" the guru Wami-Nene during the three hours of violence until midday on Wednesday, he said, adding that security forces had "acted in legitimate defence".
Lisala lies on the Congo river deep in the rainforest, some 1,000 kilometres (600 miles) northeast of the capital Kinshasa.