According to the BBC Four police officers were among those killed during Operation Containment in the Alemão and Penha districts, state Governor Cláudio Castro said. More than 80 people were arrested.
Fierce clashes erupted when about 2,500 security personnel moved in on Tuesday morning. The Red Command (Comando Vermelho) responded with gunfire, burning barricades and dropping bombs from drones, officials said.
The UN Human Rights Office said it was "horrified" by the police operation, urging "prompt and effective investigations".
The area of favelas near Rio's airport is considered to be the headquarters of one of Brazil's most powerful organised crime groups.
State officials said at least 50 of those killed were "indicated by police as suspected of being criminals".
Dozens of people were injured, including civilians caught in the crossfire.
