Whelan, a British citizen, gave himself up on July 14 after spending almost four days as a fugitive, police said. Prosecutors have accused 12 people of engaging in a criminal organization, bribery, money-laundering and tax evasion in connection with a World Cup ticket "scalping" ring.
Scalping, or the reselling of tickets for profit, is illegal in Brazil.
The Supreme Court ordered Whelan released on writ of habeas corpus on Tuesday, with the condition that he remain in Brazil while the investigation is completed and submitted to a judge. The judge will then decide whether to accept or reject the accusations against Whelan and the others.
Whelan is chief executive of MATCH Services, which won the exclusive right to sell VIP tickets for the June 12-July 13 World Cup in Brazil from FIFA, the world soccer governing body.
MATCH paid $240 million for those rights. The company, which is based in Zurich, was the main provider of hospitality packages for the Cup. MATCH said in July that all sales met FIFA rules. It denied that Whelan participated in any illegal scheme to resell tickets and said it would cooperate with Brazilian police.
Whelan, 64, was first arrested on July 7 and released on bail the next day. But prosecutors pressed for his detention, fearing he could skip the country, and a Rio judge issued an arrest warrant.
Security footage caught Whelan leaving the luxurious Copacabana Palace hotel by a backdoor used by employees just ahead of the police. Shortly afterward, he was declared a fugitive and his name was placed on an Interpol watch list.
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