A Brazilian judge accepted the indictment of Whelan and 11 others for illegally selling VIP tickets and hospitality passes to the World Cup tournament in Brazil.
Whelan, a British citizen, was first arrested on Monday but released after questioning.
His company, Match Hospitality, said at the time that Whelan did nothing illegal and that he would cooperate with police.
His whereabouts currently unknown, police chief Fabio Barucke said Whelan is now considered a fugitive.
Match Hospitality is the official FIFA hospitality provider and, according to its website, "only sells official products."