Health Minister Christine Ondoa said two family members died during the weekend not far from Uganda's capital of Kampala, and a third person in that area is suspected to have died of hemorrhagic fever, the BBC reported Thursday.
At least 17 people died in western Uganda during an outbreak in July, but Doctors Without Borders said there haven't been any cases reported since August.
Ondoa said investigators found evidence of Ebola in Luweero, about 37 miles from the capital.
Five people who came into contact with those who died are being monitored, Ondoa said.
The virus has a 90 percent fatality rate in humans, the BBC said. There is no known cure for Ebola, but patients can be treated for symptoms and pain relief.
Uganda has seen several major Ebola outbreaks during the past 12 years.