The area is known locally as favelas, with special attention to the living condition and the new coronavirus variants, a statement said on Thursday evening.
According to the city administration of Rio, the AstraZeneca vaccine will be used.
Around 130,000 people live in the Complexo da Mare.
By Sunday, more than 30,000 residents aged 18 to 33 are expected to be vaccinated.
They will then be observed for six months.
The field trial is part of a study by the Oswaldo Cruz (Fiocruz) research institute in cooperation with the municipal health authority and the non-governmental organisation Redes da Mare, the statement added.
On Thursday, Paes announced a gradual lifting of the coronavirus restrictions from September, such as allowing fully vaccinated people at football stadia and nightclubs.
Both stadia and nightclubs must operate with a maximum 50 per cent capacity. (dpa/NAN)