Whelan works for Match Services - a FIFA ticketing partner - and was one of 11 people arrested last week. He was later released without charge but had to surrender his passport as investigations continued.
Now the authorties in Brazil say he has absconded from his hotel in Rio de Janeiro - and is being treated as a fugitive.
Police investigator Fabio Barucke said that Whelan left the Copacabana Palace hotel shortly before police arrived to re-arrest him.
"He's now considered a fugitive," Barucke said. "We have security camera images of him exiting the hotel through a service door."
On Monday, Whelan was detained at the Copacabana Palace by police who seized tickets for World Cup matches; he was released early on Tuesday.
In an earlier statement, Match Services denied any wrongdoing by Whelan, and said he was willing to cooperate with any investigation, confident that it would exonerate him of any wrongdoing.
Jaime Byrom, executive chairman of Match, and Whelan's brother-in-law, said: "Notwithstanding our belief that the action taken against Mr Whelan was illegal and baseless, MATCH Services and I personally remain totally committed to assist the authorities in FIFA's fight against illegal ticket sales."