Burundi has been in crisis since April when President Pierre Nkurunziza ran for and won a controversial third term, sparking street protests, a failed coup, regular killings and a nascent rebellion.
More than 400 people have died in the violence and at least 230,000 have fled the country.
"Armed criminals arrived on a hill straddling Gacimbirigongo and ordered the locals to come out of their houses," said Celestin Singirankabo, the head of the commune of Gisozi where the town is located.
One was a local elected member from the ruling CNDD-FDD party and the other a member of a youth league, the Imbonerakure, according to two witnesses who spoke to AFP by phone.
The Imbonerakure is linked to the party in power and has been branded a militia by the United Nations.
There has been a resurgence of violence in Burundi after a relatively peaceful month with at least five people killed and some 50 injured in several grenade attacks in the capital Bujumbura this month.