The decision of Allan Turnowski to step down is being hailed by many within the country as an opportunity to stamp out corruption in the build-up to the 2014 FIFA World Cup and the 2016 Olympics and Paralympics in Rio.
Turnowski announced in a statement that he decided to step down after talking with Rio State's Security Director, Jose Beltrame.
His decision comes amid a campaign by Rio officials to break the grip violent drug gangs have on poor slums that cover large parts of the city.
Rio has promised to reduce violent crime in the build-up to the Olympics and Paralympics and the World Cup.
The 30 police officers arrested in recent days are accused of selling heavy weapons to gangs, tipping off gangs about police raids, and stealing and selling drugs, money and weapons confiscated by police.
"I feel certain this is the best decision," said Turnowski, who was in the post for nearly two years.
Turnowski's former deputy, Carlos Antonio Luiz Oliveira, was one of the officers arrested and charged with corruption, theft, and collaboration with drug traffickers.
Turnowski is the fourth police chief in five years.
Two of the chiefs were arrested, and now one has stepped down.
"The enemy now is not only the drug trafficker in the slum - it is also the police officer within the organisation that feeds that crime," Rodrigo Pimentel, a security consultant and former leader within an elite group of Brazil's military police, told Associated Press.
Rio's police are also among the world's deadliest, killing one person for every 23 they arrest, according to a 2009 Human Rights Watch report.
Beltrame said the anti-corruption operation against police will not affect the security programme in the build-up to Rio 2016.
"Changes within the team will not derail the commitment we have with society to make Rio de Janeiro an increasingly safe place," he told Associated Press.
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