Lebanon were stripped of their World Cup 9s victory over France for fielding an under age player, while a 17-year-old team-mate and two members of PNG's women's team were also banned from the tournament.
The breach by the Cedars, whose team contained no current NRL players, was detected just hours after they caused the upset of the tournament by beating England on Saturday, but their hopes of a shock semi-final berth were dashed with a loss to Wales.
Lebanon officials said Cronulla SG Ball centre Jordan Samrani broke down in tears after warming up for his international debut in front of family at Bankwest Stadium only to be told he couldn't play.
However, North Queensland-bound Jacob Kiraz lined up for the Cedars in their first game against France on Friday night, despite tournament organisers advising both Lebanon and PNG 24 hours earlier that players under 18 were ineligible.
Kiraz, who is five weeks shy of his 18th birthday, represented Lebanon in the mid-season Test against Fiji at Leichhardt Oval as International Rugby League rules allow for players over the age of 16 to play for their countries.
Orchids players Joyce Waula and Sera Koroi were also ruled ineligible.
Waula was a member of the PNG Nines team which won the silver medal at this year's Pacific Games in Samoa after being inspired to play league by her sister Vero, who was one of the first Orchids players at the 2017 World Cup.
The 16-year-old played in a recent trial against the Brisbane Broncos premiership winning NRLW team.
Koroi, 17, had taken time off school in Brisbane to play at the World Cup 9s.
PNG did not attempt to play Waula or Koroi but were unable to replace them in their squad at such short notice.
Lebanon were stripped of the two points earned for their win over France on Friday night for playing Kiraz, but the competition points were not awarded to France.
An appeal by PNG after Friday night's round of matches to allow Waula and Koroi to play was unsuccessful, with tournament organisers citing health and safety concerns.
IRL chief executive Nigel Wood said players had to be 18 to participate in the World Cup 9s at Bankwest Stadium and that was communicated to all nations.
"That's why the decisions have been taken… you'd prefer to be looking at the on-field action and not off-field stories. It's regrettable and something that everything has to learn from – tournament organisers, us as the federation and also the nations themselves," Wood said.
"At the end of the day nations have to pick players eligible."
However, a Lebanon Rugby League statement said: "The tournament manual provided to all nations prior to the tournament commencing clearly stipulates no age restriction in the RLIF eligibility rules for International Matches".
The IRL allows 16-year-olds to play internationals but they must have permission from a parent or guardian as they are under 18. In the case of the two PNG women players, they had permission.
"The rules for this tournament were clear and unequivocal. You had to be 18," Woods said, when told of some nations believed IRL laws were the standard.
"We are looking at that generally, because I think there is a little confusion. So we are working through those rules because it's in everyone's interest to be as clear as possible – and this tournament it was absolutely clear."
Wood said there would be no further consequences for Lebanon, as they had already been docked two competition points.
While IRL rules allow 16-year-olds to play, players can not debut in the NRL or NRLW until they have turned 18.
With the majority of the players in the World Cup 9s from the NRL and Super League competitions, tournament organisers were concerned about players yet to turn 18 playing against professionals and semi-professionals.
The Cedars, whose squad did not include any current NRL players, shocked England 16-13 on Saturday and after beating France on Friday night only needed to win against Wales to ensure a stunning semi-final berth.
However, Lebanon coach Rick Stone refused to blame the drama within the Cedars camp over the banning of Kiraz and Samrani for their loss to the Dragons.
"We were struggling for players actually when we selected our squad and we ended up having two players who were under the age of 18," Stone said.
"Obviously we couldn't play them. It wasn't a big issue, it didn't change too much for us. We played everyone in the game that was over 18 and we weren't good enough.
"We were a little bit tired. We're a pretty young side, been up for the first couple of games and probably lacked a little bit of zip and energy in that game [against Wales]. That's just the way it goes."
Lebanon and PNG officials did not become aware of any eligibility issues until Thursday night and it was too late to call in replacements.
"Jacob Kiraz played for us in the June Test and we were under the impression the rules were going to be the same," Stone said.
"Obviously the NRL is running the game on behalf of the international body and you have to be 18 to play in the NRL and they've obviously transferred those rules across.
"We didn't have to make any changes to our team because those boys hadn't played yet. That was the story."
The Cedars are rebuilding ahead of the 2021 World Cup after the retirement of Robbie Farah and Tim Mannah, while some other NRL players did not play due to a dispute with the Lebanon board.
Stone said he hopes the issue can be resolved soon.
"We'd all love to see that," he said. "We've got to a position where we've probably got 10 players who are playing in the NRL of Lebanese descent. They're eligible to play for us and it'd be great to see those boys playing with some of the young blokes."