Some 20-30 Allied Democratic Forces [ADF] fighters crossed the Semiliki River into Uganda's southwestern Ntoroko district on Monday night, sparking a firefight with Ugandan soldiers, the Uganda People's Defence Forces (UPDF) spokesman Felix Kulayigye wrote on Twitter.
"Our intelligence got wind of them and they were intercepted. A fight is on to decisively deal with the group. 11 of them have been (killed)," he said, adding that a further eight had been captured, while one Ugandan soldier died.
The ADF shot at civilians in the area, injuring at least three people, while several residents fled their homes to seek shelter in urban areas, the Kampala-based Daily Monitor newspaper reported.
Following a series of bombings in and around Uganda's capital late last year, Kampala deployed hundreds of troops to eastern Congo as part of a joint operation with Congo's army to root out the ADF.
Uganda says the operation has recorded significant successes, but the armed group has continued to attack civilians.
The Allied Democratic Forces (ADF), which pledged allegiance to Islamic State in 2019, started as an uprising in Uganda but has been operating in the dense forests of eastern Congo since the late 1990s, where it has killed thousands of civilians.
In a separate arrangement last month, Uganda said it would deploy an additional 1,000 troops to join a regional force mandated to help end decades of instability in eastern Congo.