The Botswana government has previously turned a blind eye to discrimination and violence meted out against gays in the country.
Botswana’s constitution outlaws same-sex sexual acts between consenting adults.
But in a sign that the official tide is turning, Masisi condemned violence against gays, lesbians and transgenders.
Officially launching the 16 Days of Activism Against Gender-based Violence in the capital Gaborone, Masisi encouraged people in same sex sexual relationships to report abuse to the police.
He said his administration has adopted the national policy on gender development as part of efforts to end gender-based violence in the country.
Recently a social media video of a transgender woman being brutally beaten up and abused by a mob in Botswana was condemned by activists.
The video showed the woman being violated by members of the public, including women and security guards, while she helplessly lay on the ground exposed.
Botswana is one country in Africa where officially at least the LGBT community is being protected.
Across Africa, the trend remains the same as both legislation and official policy continue to forced gays and lesbians underground.