Namibian President Hage Geingob was sworn in at Windhoek on Saturday.
Botswana’s director of health services had placed Masisi “on self-isolation for a period of 14 days starting March 21 following his trip to” Namibia, Botswana government said in a statement posted on its Facebook page.
Namibia has registered just three “imported cases, and is considered low risk for (Covid-19) transmission”, said a government statement.
But there was a “high probability of undetermined local transmission” because of the low rates of testing in southern Africa, the statement added.
Masisi will work from his official residence, isolated from his family. Members of his entourage who accompanied him on the trip will respect the same restrictions.
Botswana is one of the few African countries that has not yet officially recorded a single coronavirus case, as continental numbers rose to more than 1,000 cases at the weekend.
As part of a slew of measures to avoid the spread of the virus to the diamond-rich country, Masisi last week suspended all external trips by public officers.
The government justified the Namibia visit, calling it an “emergency official” trip for face-to-face talks with his counterparts to discuss “urgent border matters” in the light of the spread of the virus.
Zimbabwe’s President Emmerson Mnangagwa and Angola’s President Joao Lourenco also attended the ceremony in Namibia — despite having declared strict travel restrictions in their countries.
The ceremony, at the presidential palace, was attended by several hundred other guests despite official restrictions on public gatherings to a maximum of 50 people.