The Red Cross has launched a search and rescue operation with the police, military and community members in 12 affected areas but it is not yet clear how many people are missing.
Rain is hampering communication in the remote location, on the border with DR Congo and separated from the rest of Uganda by the Rwenzori mountains.
At least 20 people have been killed as a result of floods and mudslides in the last week in Uganda.
The extreme weather has been blamed on the Indian Ocean Dipole — a climate system defined by the difference in sea surface temperature between western and eastern areas of the ocean.
At the moment, the ocean around East Africa is far warmer than usual, resulting in higher evaporation and moist air flowing inwards over the continent as rain: the hallmarks of a “positive” dipole.