The virus has killed two members of the same family since Saturday about 50 kilometres (30 miles) from the capital Kampala, health minister Christine Ondoa said.
"The ministry of health would like to inform the general public that another viral haemorrhagic fever, Ebola, has broken out in the country," Ondoa said.
A third man also died in the area late last month after showing symptoms of Ebola however no samples were taken from the victim and the case was not reported to local health officials, the minister said.
So far five people who came into contact with the deceased are being monitored, with two admitted to the isolation unit at Kampala's main Mulago hospital, she said.
The new cases come just weeks after an Ebola outbreak in western Uganda that claimed at least 17 lives was officially declared over following a 42-day surveillance period mandated by the World Health Organisation during which no new cases were reported.
Since then an outbreak of another similar virus, Marburg haemorrhagic fever, in southwestern Uganda has killed at least eight people.
Health officials say there is no evidence that the latest Ebola cases are related to the previous outbreak.
Ebola, which spreads by contact with the blood or other bodily fluids of infected people or corpses, is fatal in between 25 and 90 percent of cases according to WHO, with victims in the most severe cases bleeding from body orifices before dying.
The rare haemorrhagic disease killed 37 people in western Uganda in 2007 and at least 170 in the north of the country in 2000.
In neighbouring Democratic Republic of Congo the latest outbreak of Ebola around the northeastern town of Isiro, some 350 kilometres (220 miles) from the Ugandan border, had claimed 26 lives by late October, when the WHO said the outbreak had stabilised.
DR Congo has recorded eight outbreaks of Ebola since the virus was first reported near a Congolese river that gave the disease its name in 1976.
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