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Legio Monteiro is head of the Vigilant Non-Compliant Citizen's Movement, which is considered close to the ruling PAIGC party and which is campaigning to end a long-running political crisis between the party and the president.
Monteiro was struck on the head and body and his injuries are being treated at a secret location, sources close to him said, adding that his life was not in danger.
The tiny west African state has been in the grip of a power struggle since August 2015, when Vaz sacked then premier Domingos Simoes Pereira, leader of the African Party for the Independence of Guinea and Cape Verde (PAIGC).
A new prime minister, Umaro Sissoco Embalo, was sworn in last December but PAIGC rejected him, accusing Vaz of breaching an agreement calling for a consensual choice of prime minister.
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Last week members of Monteiro's group were badly beaten by police during a protest march, attended by PAIGC officials.
"The struggle will continue despite these attacks on our members," Sana Cante, the movement's coordinator told AFP.