Locals have likened the hillside area – home to about 300,000 people – to a “war zone” since the operation began.
Roads remain closed throughout the region.
The Red Command group have been expanding their territory across the Rio state, increasing drug trafficking routes and control of the hillside favelas.
Rio’s police said more than 200kg (441lb) of drugs were seized in the raid, along with dozens of firearms.
The joint operation by civil and military police comes after a year-long investigation.
Dozens of the suspects are thought to be members of a faction from the Pará state who are currently hiding in Rio de Janeiro.
Large-scale police operations are not uncommon in Brazil ahead of major international events in the South American nation.
The UN climate summit COP30 is taking place in the northern city of Belem in November.