A magnitude 6.5 earthquake struck nearly 250 km north-northwest of the Botswana capital Gaborone on Monday, at depth of 12 km (7 miles), the U.S. Geological Survey said.
Tremors were also felt in neighbouring South Africa.
"We certainly felt it here in central Gaborone," Jeff Ramsay, Botswana's chief government spokesman, said.
"I'm not aware of damage yet, it is too early to say. The buildings here in the enclave certainly were trembling.
"I'm not sure where the epicentre was yet and that could be critical. I wouldn't be surprised if some place there was some type of damage."
The USGS revised the depth of the quake from 35 km.