Waldomiro Costa Pereira was killed after the men burst into the building in the state of Para and surrounded guards, campaigners said.
Mr Costa Pereira was an activist with the Landless Workers Movement (MST).
He frequently demonstrated in support of land reform in Brazil.
The MST wrote in a statement that it was "with immense sadness that we mourn his death" adding that the group stood "in solidarity with his wife, children and all his family in this moment of pain".
Mr Costa Pereira was also a member of Brazil's Workers' Party.
