"Since the operation began we have killed 75 attackers," army spokesman Ninsiima Rwemijuma in the Rwenzori region told AFP.
Five soldiers, five policemen and 11 civilians were also killed, making up a total of 96 dead in the mountainous and rural region which borders Democratic Republic of Congo.
Attackers, who police said were armed with machetes, spears and guns, launched a series of surprise attacks Saturday and Sunday, with the army sending in extra troops.
"We expect no more civilians dying because we have deployed enough forces on the ground and neutralised attacks," Rwemijuma said.
Ugandan police say the attacks are ethnic battles, with the local majority Bakonzo people trying to kill the minority Basongora people, because of "long-standing differences of culture and over land," police spokesman Fred Enanga told AFP.
"There is a tribal conflict, some of the Bakonzo do not want the minority groups recognised as kingdoms within what they perceive to be the larger Kingdom of Rwenzori, with Bakonzo the dominant tribe," Enanga added.
"The number of the attackers killed during contact with our forces or dying due to wounds may go up," Rwemijuma said.
"Some may have escaped with gunshot wounds, and that is why we are engaging sniffer dogs to flush out those who may be injured and hiding, or just hiding to avoid detection."
Security forces have arrested over 80 suspected fighters.
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