Hilton will likely be replaced by Ricardo Leyser, a senior official in the sports ministry who has been managing Olympic preparations, Wagner said in a wide-ranging news briefing with foreign media in Rio.
Hilton could not immediately be reached for comment. But Ugo Braga, an aide of his, said President Dilma Rousseff told Hilton her decision in a meeting on Tuesday evening.
His departure came after Hilton quit his Brazilian Republican Party (PRB), which was part of Dilma Rousseff's ruling coalition, on Friday. The PRB broke with Rousseff's governing coalition last week and the minister quit the party to keep his post.
Rousseff, who is trying to keep her coalition together as she battles impeachment proceedings, pushed out Hilton in a bid to woo back the PRB, several party members said on condition of anonymity because they were not authorized to speak publicly about the matter.
Hilton's departure is a sign of how the fallout from Brazil's spiraling political crisis could affect the country's preparations for South America's first Olympics in August.
Appointed in January 2015, Hilton had been criticized for an apparent lack of sporting experience. In his acceptance speech he said, "I may not profoundly understand sport, but I understand people, I know how to listen."
Hilton's likely successor, Leyser, has been responsible for coordinating the organization of Rio 2016 Olympic Games within the ministry. Except for a brief six-month hiatus, he has been the ministry's secretary for professional sport since 2009.
(Reporting by Maria Pia Palermo and Anthony Boadle in Brasilia; Editing by Richard Chang)
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