Mugabe, 93, arrived on Wednesday evening. He was accompanied by nine cabinet ministers and other Zimbabweans.
The nonagenarian will join several regional leaders, including former president Thabo Mbeki and Lesotho’s King Letsie III.
The Zimbabwean leder and Masire shared a special bond and Mugabe frequently visited his Botswana counterpart between 1980 to 1998, the report said.
Masire died in hospital last week at the age of 91.
Masire was the president of Botswana from 1980 to 1998.
He led various diplomatic initiatives in Africa, including chairing a panel that investigated the 1994 Rwanda genocide, and co-ordinating the Inter-Congolese National Dialogue.
Reports said that Mugabe had not yet offered any public condolence message to Botswana since the death of Masire.