Ponga shocked league officials on Tuesday when he announced via the Knights' website he did not want to play in the end-of-year Tests  instead prioritising his club's pre-season training.
The fullback claimed he wanted his full focus to be on winning the Knights a premiership and proving himself to be a Newcastle great.
However NRL rules dictate players must make themselves available for all representative fixtures, unless injured, including Test football.
Ponga was believed to be in the mix to be named in Meninga's squad for the Pacific Championships, starting October 18.
Meninga said on Wednesday he had spoken to the 26-year-old and while he understood Ponga's motivation was still disappointed by his call.
"Playing for the Kangaroos is the pinnacle of the game in this country," Meninga said in a statement.
"I was disappointed not only that Kalyn made the decision that he was unavailable for the Kangaroos, but also the process which led to the decision and the announcement.
"I have spoken to Kalyn since and while I understand his intent, it doesn't erase the disappointment in the decision."
The ARL Commission has made a point to make international football a key focus, with Peter V'landys declaring this week he wanted the Kangaroos jersey to be the pinnacle again and the Pacific Championships a successful venture.
Meninga said he was happy to have the support of the chairman.
"I'm pleased that Peter V'landys has come out so strongly and I support the game in ensuring that there is a proper process around players being ruled out of playing for their country," he said.
Ponga made himself unavailable for State of Origin selection last season, but that came after a long stint out following a concussion.
There are no such injury concerns this time with Ponga confirming in an interview on SEN radio on the weekend he was fit to play for Australia.
But he backflipped on Tuesday.
"I want to win a comp, for me anything short of that isn't success," Ponga said.
"My focus has never shifted from wanting to win a premiership with the Knights, that has been my goal since I joined the club in 2018 and continues to be my focus.
"When I'm done, I want to look back at my career with a positive reflection, including people saying he was a great signing and represented our community to the best of his ability.
"For now, I don't feel like I have earned that yet. That's why I have made this decision and will work hard every day to chase those goals."
The NRL could still seek further information from the Knights, with the potential of sanctions for not making a player available for selection without a valid reason.
The Queenslander's withdrawal means James Tedesco has firmed to retain his spot as Australia's fullback and captain for the Pacific Championships.
The Sydney Roosters captain was dropped from NSW's State of Origin side this year but his replacement Dylan Edwards has since battled a knee injury and there is every chance he could be ruled out of the post-season Tests.
Tedesco, meanwhile, delivered arguably his best match of the season to overcome Manly and steer his team into the preliminary final.
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