In a televised address on Wednesday, Mr. Museveni said the ban will take effect immediately. This includes the ubiquitous boda-bodas, as the motorcycle taxis are locally known.
Private cars will only be allowed to carry three passengers including the driver.
Uganda has 14 confirmed cases of coronavirus, including an eight-month-old baby girl.
With news that some Ugandans who have never left the country are now contracting the virus, authorities want to limit movements within towns and between regions.
Markets, which are often big and overcrowded, will only be allowed to sell food.
Last week, Mr. Museveni announced the closure of all schools, bars, cinemas and banned public gatherings for 32 days.
Public transport workers are a powerful political constituency, numbering tens of thousands in the capital, and the president is often careful not to impose restrictions on them.
It might explain why this suspension is only for two weeks.