Papua New Guinea Football Association (PNGFA) president David Chung resigned from the post when he quit the presidency of the Oceania Football Confederation (OFC), the PNGFA says.
Chung stepped down from the OFC last Friday two days before a meeting of the OFC executive when it was understood he would face a vote of no-confidence.
On Monday, OFC announced an internal investigation into potential wrongdoings after an audit ordered by world football's governing body, FIFA, identified possible fraud in a project to build a new headquarters for the OFC in Auckland.
The New York Times reported the audit found Chung had hired, without issuing a tender, a company to construct the headquarters which had no experience of the work required.
It found a separate company set up by Chung might have had links to one hired to work on the project.
PNGFA senior vice president John Wesley Gonjuan declined to comment on Chung's resignation to RNZ Pacific but it is understood Gonjuan is acting as the organisation's president.
In a statement, Gonjuan thanked Chung for a number of initiatives including bringing the U-20 Women's World Cup to Papua New Guinea in 2016 and for developing the PNG's National Soccer League, NSL.
The league broke into two last year after Chung's opponents alleged he blocked votes for rival John Kapi Natto in the PNGFA's 2016 elections.
The rival National Premier League set up by the Football Federation PNG had since attracted 12 teams while only six teams competed in the NSL in 2017.
The NSL playoffs were controversially cancelled last year and further evidence of problems in the league have emerged in the National newspaper.
When contacted by RNZ Pacific, PNGFA general secretary Dimirit Mileng refused to explain the issues.
"That is our problem we will sort it out ourselves. Why would you want to know? We are managing our own issues the best way we could," Mileng said.