The East African nation has been on high alert, amid fears that the viral haemorrhagic fever could spread from DRC which is battling an outbreak.
Parts of Uganda’s western border are about 100 km (62 miles)from sites of an Ebola outbreak taking place in Congo.
The security situation in North Kivu and Ituri is hindering effective implementation of response activities.
Health Minister Jane Ruth Aceng said authorities would administer about 2,100 vaccinations covering so called frontline health personnel working in districts near the border.
Tens of thousands cross the border in both directions weekly for trade and family visits and other purposes, Aceng said.
Because of this the “risk of cross border transmission was assessed to be very high … hence the need to protect our health workers with this vaccine,” she told a news conference.
Congo declared an outbreak of Ebola on Aug. 1 and there have been at least 139 deaths.
Because of the short distance from the outbreaks in Congo, Uganda which has suffered regular outbreaks of Ebola and Marburg over the years, has heightened screenings of arriving travellers and training of health personnel in border areas.
Aceng said widespread insecurity in eastern Congo’s North Kivu and Ituri provinces added to Uganda’s vulnerability to cross border transmission.
“The security situation in North Kivu and Ituri is hindering effective implementation of response activities,” Aceng said.
Uganda’s worst Ebola outbreak was in 2000 when 425 people were infected, more than half of whom died.