This precaution is being taken because the health care officials are anxious that the infection would spread into the country from the borders shared with Democratic Republic of Congo.
The World Health Organization, CDC and other worldwide health organizations say they are anxious about the current Ebola outbreak spreading to port cities like Butembo, which will only exacerbate infection transmission rates.
According to Congolese health authorities, the latest victims to be infected with the virus are a newborn baby and the mother.
The vaccine that is being administered is still experimental but has been shown to be protective in the clinical trials.
This particular vaccine is now being administered in DRC and is demonstrating positive protective results and potency against the Ebola virus-Zaire type.
Ebola is a deadly disease caused by a virus, though there are five strains, and four of them can make people sick.
A World Health Organization assessment of the situation in DRC released on 22 October, warned of the potential for the virus to spread into Rwanda, South Sudan and Burundi, as well as Uganda, and called on these countries to step up readiness efforts.
Yonas Tegegn Woldemariam, WHO country representative in Uganda, told newsmen that the operation kicked off in Uganda's western district of Ntoroko.
"Therefore, the rVSV-Ebola vaccine is not available to the general population at this stage".
Uganda on Monday said Ebola vaccinations for frontline health workers in high-risk districts bordering the Democratic Republic of Congo (DRC) have been postponed to Wednesday due to training of vaccination staff. The affected areas in the DRC [North Kivu and Ituri provinces] are about 100km from Uganda's border districts.
Other preparatory activities underway in Uganda to prevent the spread of the disease include health facility and community-based surveillance; collection and testing of blood samples; and cross-border monitoring.
"Uganda has taken a very huge step in mitigating the risk of Ebola among health workers". An outbreak in the western part of the country was declared over in July, after infecting 53 people and killing 33.Just days later, the current outbreak was discovered across the vast Central African nation, in a region that has been at the heart of multiple conflicts.Maggie FoxMaggie Fox is senior writer for NBC News and TODAY, writing top news and analysis on health policy, science, medical treatments and disease. The worst outbreak was in Uganda in 2000 and 2001, when 574 people were infected and 261 died.
The current Ebola outbreak is unfolding in an active war zone with several armed groups attacking health officials, government aids and civilians.