The elderly Irishman was arrested in his dressing gown during a dawn raid at his luxury beachfront hotel on Wednesday, where Hickey had been staying with his wife and fellow IOC members.
Police said they had discovered evidence linking Hickey to an international scheme to illegally pass tickets to touts who were reselling them at well above their original price.
The 71-year-old, frightened by the raid according to a police chief, was first taken to Samaritano hospital after complaining of chest pain.
He stayed overnight before being released into police custody on Thursday and taken in a wheelchair to a police station for questioning.
Hickey was denied bail by a Brazilian judge and transferred to Bangu, a penitentiary complex which houses some of Brazil's most dangerous inmates.
With more than a dozen separate units in the city's rough western area, Bangu is notorious for violence and prison riots.
However, it's likely that Hickey, like other high-profile prisoners who have been held in Bangu, is in one of the safer areas separated from the general penitentiary population.
Those units do not have the extreme over-crowding and violence of the others - but are bleak nonetheless.
The Olympic Council of Ireland (OCI) said on Friday it would commission an independent investigation into the accusations that led to the arrest of its longtime president.
Hickey has temporarily stepped down from the OCI and from his role as the president of the European Olympic Committee (EOC) during the investigation.
The OCI also said it would scrap a previously announced internal inquiry, in a complete U-turn only days after saying no independent monitoring of its investigation was needed.
"The OCI confirms that it will cooperate fully with any state inquiry into its handling of ticketing arrangements for the Rio Olympics," it said in a statement.
Police this week also issued arrest warrants for three executives of Dublin-based PRO10 Sports Management.
They are recommending charges against Hickey and the executives for illegal ticket resale, criminal association and fraudulent marketing. Prosecutors have yet to decide on any charges.
Ticket touting is illegal in Brazil and police and prosecutors have been cracking down on the practice since the country has hosted the globe's two biggest sporting events, the 2014 World Cup and now the Olympics.
During the World Cup, police arrested high-level figures of the official Cup corporate hospitality provider for funnelling tickets to touters. At that time, authorities estimated the touting ring was making 1 million reais ($310,000) per match.
