Police fired tear gas as they dispersed the crowd outside the capital, Kampala. Gunfire was heard but it was not clear if live rounds or rubber bullets were fired.
Doctors Without Borders said more than 687,500 displaced people were now living in camps or with host families where MSF treated at least 11,220 children suffering from malnutrition, 2,310 victims of sexual violence and 1,980 wounded.
The Congolese rights group said that rebels from the Allied Democratic Forces had killed at least 43 people since Friday in and around Beni, the epicentre of the ongoing Ebola epidemic.
Many Rwandan refugees continue to refuse returning home despite a UN decision to terminate their refugee status. They fear state reprisals but Kigali says only those with 'criminal records' aren't returning.
"We have recovered 12 bodies from the water and one person has been rushed to hospital with serious injuries," says Red Cross branch manager in the Bundibugyo district.
Fatalities were caused by police firing on protesters in eastern Democratic Republic of Congo. A senior UN official responded to the protests and attacks against peacekeepers and Ebola health workers, saying they were planned, organised and funded.
Juvenal Musabimana, also known by his nom de guerre Jean-Michel Africa, killed alongside four of his bodyguards following a firefight in Democratic Republic of Congo's North Kivu province, army officials say.
The latest casualty in Uganda was a nine-year-old girl from the DRC, reviving fears that the virus could cross the porous borders of the central African country.
The virus has killed more than 1,700 people in the Democratic Republic of Congo since the world's second-worst outbreak was declared almost a year ago and is threatening to spill over its borders.
Restrictions on travelling to the Democratic Republic of Congo would "impede our ability to effectively control" Ebola virus, Dr John N Nkengasong, a top health officer at African Union said.
Ugandan pop star-turned-leading opposition figure Bobi Wine said he was ready to take on veteran President Yoweri Museveni in the 2021 elections.
Democratic Republic of Congo recorded 2,382 cases of Ebola, of which 1,606 were fatal, the Health Ministry says.
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