David Chung abruptly resigned as FIFA's senior vice president and a member of its ruling council on Friday.
His decision comes after an audit of the Oceania Football Confederation (OFC) he led found "potential irregularities" on a $20 million building project and funding was cut to the region by soccer's world governing body.
Chung quit after seven years as OFC president for what were described as "personal reasons."
IFA acknowledged later in the day it has concerns about the management of the OFC under Chung but did not accuse him of wrongdoing.
The resignation followed an investigation ordered by FIFA into the construction of a new headquarters for the OFC in Auckland, New Zealand.
"OFC has been recently the subject of a review conducted by an external audit firm on FIFA's behalf," FIFA said in a statement to The Associated Press.
"It has shown potential irregularities in the construction process of the OFC Home of Football.
"The review findings, which were not focusing on specific individuals, led to the temporary suspension of funding to OFC. The process is now ongoing and the FIFA administration will continue to support OFC in building and improving their internal controls."
FIFA, which provided $16.8 million in funding to the OFC in 2017, would not say whether any specific individuals are being investigated.
The OFC, whose executive committee is due to meet on Sunday, has not published any annual accounts on its website since 2015.
Chung had been FIFA President Gianni Infantino's highest-ranking deputy until Friday's abrupt departure as one of the most powerful figures in world soccer.
He is still listed by FIFA as president of the Papua New Guinea Football Association, a position he was elected to in 2004.
Chung succeeded Reynald Temarii, who was forced out of the OFC presidency in 2010 after being caught in an undercover sting into World Cup bid vote-buying.
In 2015, Temarii was banned from soccer for eight years in a separate ethics case.
