Museveni's consultant physician, Joseph Okiria, tweeted on Friday that the aides had tested positive on their return with the President from trips to the United Arab Emirates and Ethiopia, reports Xinhua news agency.
"Following President Museveni's recent return from Dubai, Abu Dhabi, and Addis Ababa, three presidential aides have tested positive for Covid-19. This despite best efforts and measures including daily PCR testing and full vaccination," Okiria said.
He said the staff who tested positive had been isolated and were receiving care.
"The President and other members of the team tested negative and will be retested," Okiria added.
"This highlights the continued difficulty of safe travel during the pandemic and the importance of testing all inbound and outbound travellers," the physician added.
The number of daily infections in the east African country continued to drop, with less than 100 cases being registered, according to the health ministry.
The Ugandan government recently decided that incoming and outbound travellers would be tested for Covid-19.
Till date, the country has registered a total of 124,437 coronavirus cases, 3,172 deaths and 96,237 recoveries since the outbreak started in March 2020, according to the Ministry of Health.