"We are seeing a downward trend in the number of cases," Health Minister Jane Ruth Aceng said on the local NTV news service late on Wednesday, citing the absence of new cases in the two districts over many days.
"We are also not seeing new cases in Kampala, in the greater Kampala metropolitan area, neither are we seeing cases in Masaka and Jinja," two other cities, she said.
Health Ministry spokesperson Emmanuel Ainebyoona told Reuters on Thursday that Mubende had gone for at least 16 days without a new case.
The development is a major sign the East African country is having a measure of success in efforts to combat its latest outbreak of the deadly hemorrhagic fever disease more than two months after it was declared.
Central Uganda's Mubende district was where the outbreak was originally declared on Sept. 20. It and another district, Kassanda, are considered to be the epicentres for the disease's spread. Movement in and out of them has been restricted.
The Ebola virus circulating in Uganda is the Sudan strain of Ebola, for which there is no proven vaccine, unlike the more common Zaire strain, which spread during recent outbreaks in neighboring Democratic Republic of Congo.
But three candidate vaccines against the Sudan strain are planned for a clinical trial in Uganda.
The country has so far recorded 141 cases and 55 deaths, according to the ministry.