Health Minister Ruth Jane Aceng told AFP on Saturday that "the lockdown of Mubende and Kassanda districts ... will be extended for another 21 days."
"We urge the public to comply and remain vigilant," she added.
The lockdown includes a dusk-to-dawn curfew, a ban on personal travel and the closure of markets, bars and churches.
According to Uganda authorities, 51 deaths reported had been reported as of Saturday.
Since the outbreak was declared in the central district of Mubende on September 20, the disease has spread across the East African nation, including the capital Kampala.
The strain now circulating in Uganda is known as the Sudan Ebola virus, for which there is currently no vaccine, although there are several candidate vaccines heading towards clinical trials.
President Yoweri Museveni imposed a 21-day lockdown on Mubende and neighbouring Kassanda on October 15 but has said that nationwide curbs were not needed.
Museveni has also ordered the police to arrest anyone infected with Ebola who refuses to isolate.
The World Health Organization (WHO) on Wednesday said Uganda had registered over 150 confirmed and probable cases, including 64 fatalities.
Uganda's last recorded fatality from a previous Ebola outbreak was in 2019.