Chile's investigative police had served Jadue a subpoena on Friday, hours after he announced he would take a 30-day leave for medical reasons, as part of what the ANFP said was an investigation into how it allocates salaries.
The ANFP said Wednesday evening that it had accepted Jadue's resignation as president of the association.
Under the flashes of cameras and with police escorts, Jadue boarded a flight in Santiago late on Tuesday night, bound for New York via Miami, local media reported.
A spokeswoman for the Chilean police force declined to comment.
South American football confederation CONMEBOL and the sport's world governing body, FIFA, are reeling from a corruption scandal. Several leading directors were among 14 FIFA officials and sports marketing executives indicted in May in a probe led by the U.S. Federal Bureau of Investigation into allegations of bribery, money-laundering and wire fraud. A majority were from South America.
Local newspapers La Tercera and El Mercurio quoted unnamed ANFP officials as saying that Jadue was planning to collaborate with the FBI investigation.
"It's not a holiday," El Mercurio cited one official as saying. "He is due back May 10 next year. Jadue is travelling as a protected informant of U.S. justice.
(Reporting by Anthony Esposito; Editing by Lisa Von Ahn, Andrew Hay and Steve Orlofsky)
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