The attack began on Saturday and targeted three districts in Uganda's remote western regions along the border with Democratic Republic of Congo (DRC), the army said.
Insurgents using submachine guns and machetes attacked police and military posts in Bundibugyo, Kasese, and Fort Portal districts, killing at least one civilian and one soldier.
An army official in Bundibugyo told AFP it was a group seeking to "acquire weapons to start a tribal militia," but that it had been pushed back by security forces.
The attack was led by a man named Christian Asuman Muganzi, a "traditional herbalist", said Albert Kaliruga, deputy head of security for the region.
He was cornered at his hideout in Kakuka, Bundibugyo on Tuesday and killed along with "over 20" of his fighters, Kaliruga told AFP, with 15 others arrested.
"He was using his shrine at Kakuka to indoctrinate and recruit people to join his criminal group," Kaliruga said.
"At his shrine, we recovered traditional herbs, fetishes and other items he has been using to indoctrinate his recruits and apparently to protect them during battles," he added.
Uganda faced years of barbaric insurgency led by cultish militant Joseph Kony through the 1990s and 2000s.
There are persistent threats along its western border with DRC, a remote and lawless region home to multiple militias, including an affiliate of the Islamic State group.
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