The chief said he thought rogue police officers were to blame in what is the worst death squad massacre in the violence-torn Brazilian city in more than a decade.
Men, women and children were randomly killed in the shooting spree on Thursday night in Baixada Fluminense in Rio's rough north side.
The victims included a civil servant drinking in a bar, a boy playing pinball, a cook on his way home from work and a transvestite prostitute, morgue officials said.
Marcelo Itagiba, Rio's public security secretary, said police likely carried out the killings as a reprisal for the arrests earlier on Thursday of officers suspected of a separate double murder.
The arrests were part of a crackdown on death squads formed by police officers carrying out criminal acts.
In one case, police were filmed throwing the decapitated head of one victim over the back wall of a precinct house.
"The Security Secretariat is working with the strong hypothesis that this massacre was an act of reprisal for operation Navalha na Carne that resulted in the arrest of eight military police who are suspected of a double homicide near the Duque de Caxias precinct headquarters," Itagiba said in a statement on Friday.
Because of their rigid organisational style, Brazil's street police are known as military police but they are not affiliated with the army or federal government.
Violent crime and feuds between
gangs plague the city
Witnesses to the latest shooting said the armed men fired at random, leaving victims no time to escape.
"It was very quick. I got up to my house and went down the hallway when I heard a rain of gunfire. We were stunned. When we arrived, the car had already left," Creuza Regina, the grandmother of one victim, said.
This was the worst urban massacre in more than a decade in Brazil. In 1993, 21 people were murdered in Rio's Vigario Geral by a death squad made up of police.
"Any hopes that such actions were horrors of the past have been dashed by the events of last night, which show the lengths that Death Squads will go to in order to spread terror and resist attempts by the authorities to stop their activities," Amnesty International said in a statement.
Family members expressed outrage.
"The situation is getting much worse. The control of public authorities over the situation is very precarious"
Jose Vicente da Silva Filho
"I'm in shock. My nephew was playing with his cousin and was brutally assassinated," said Angelo Soares, uncle of a 14-year-old victim.
Public security experts called Rio a powder keg. Violent crime plagues the city, with rival drug gangs controlling many slum areas, known as favelas, and defying authorities.
"The situation is getting much worse. The control of public authorities over the situation is very precarious," Jose Vicente da Silva Filho, a former National Security Secretary and police commander, said.
International human rights groups often criticise Rio police and say they have a history of summary executions. Security officials said police killed 983 "suspects" last year and 1195 in 2003.
Police experts blame poor management, outdated anti-crime tactics, corrupt officers who cooperate with drug runners, and poorly paid, risky work that can encourage criminal behaviour.
Last year, about 50 Rio police were killed in the line of duty.
"Rio is the biggest security problem in the country," Silva Filho said.