Yoweri Museveni, Uganda's president, has visited some of the villages in the region by helicopter, ordering remaining residents to move away from sliding hillsides.
Military transports have also begun ferrying residents to an area about 20km away.
Museveni said settlements in the flood valley of the nearby River Manafa had left many people particularly vulnerable, and also blamed farmers for stripping the land clear of thick plant life that retains water.
Last Monday, rains triggered massive landslides that buried three villages in the Bududa region, burying what officials estimate to be several hundred people.
Rescue crews in the remote district, unreachable by road, are using hand tools to dig through thick rivers of mud left in the wake of the disaster.
Villagers in the Bududa region have recovered 92 bodies so far but were unable to continue searching on Friday because of the rain, said Kevin Nabutuwa of the Uganda Red Cross.
"Thousands of people have been displaced by floods. We are advising them to relocate to high, dry areas as we mobilize for assistance," said Dorothy Florence Hyuha, a member of parliament from eastern Uganda.
An official from the Ministry of Disaster Preparedness said a rescue team had been sent to affected areas.