The Football Federation of Papua New Guinea (FFPNG) may call for an investigation into the PNG Football Association (PNGFA), its president says.
FFPNG was launched in 2016 after a number of local associations split from the PNGFA which was then run by David Chung.
Chung resigned from the PNGFA this month and from his post as president of the Oceania Football Confederation (OFC) which is now investigating possible fraud.
The FFPNG is not recognised by OFC and by extension football's world governing body FIFA.
However the FFPNG president, John Kapi Natto, said he would ask for the investigation to extend to the PNGFA if the two bodies could not reconcile through dialogue.
"They need to come and sit down with us and find a way to resolve it. If we cant find a way to resolve it my last resort is to file complaints and documents to OFC," Natto said.
"I want to call for an investigation of David Chung right into PNG football because we need to clear the house."
The PNG government had also called for dialogue between the FFPNG, which has 12 associations and PNGFA which has six, Natto said.
"The government has welcomed the resignation of Mr Chung. They've also asked us to come together and mediate," he said.
"I have about 12 associations who have gone away because of the way the (PNGFA) congress was held in 2016. Because Mr Chung was in office in OFC and FIFA my complaints could not go to the respective offices for them to look into the problem that we had."
As well as the problem that led to the split, irregularities with PNGFA projects in Chimbu and Kimbe needed to be addressed, Natto said.
"Then we've got a project in Bougainville by FIFA and by PNGFA for I think 1.6 million (Kina). I actually visited the place where the ground breaking ceremony was and there was tall grass going in that place. There was not even a project," he said.
"For me, I want to see that investigation in Oceania Football come all the way down to Papua New Guinea Football."
The 11-0 thrashing of PNGFA team Toti by New Zealand's Team Wellington in this month's quarterfinals of the OFC Champions League was symptomatic of the sport's issues, Natto said.
"I'm doing my best with the 12 associations of the Football Federation of Papua New Guinea. We want to do things right. We want to have proper administration that is accountable, that is transparent," he said.
"So if Mr John Gonjuan from PNGFA does not want to understand things like that it's going to be indicated in our teams that go out and play in the Champions League."