Melbourne City duo Lawrence Wong and Medin Memeti, along with Adelaide United's Amlani Tatu, have all been made unavailable by their clubs for the qualification window which kicks off against hosts Laos next Monday.
The Young Socceroos are reigning Asian champions after claiming the 2025 tournament in what represents just Australia's third continental title at any age group since switching from Oceania to the Asian Football Confederation in 2006.
Australia face Laos (August 31), Malaysia (September 3) and Indonesia (September 6) across the space of a week where only a first-place group finish will guarantee qualification for the under-20 Asian Cup in China in 2027.
The under-20 Asian Cup doubles as a qualification pathway for the under-20 World Cup, which Australia reached for the first time in over a decade last year.
But Wong, Memeti and Tatu were not granted releases by their clubs for the critical qualifiers.
Sources spoken to by AAP were perplexed at the club's respective decisions given Australia's domestic players are in the midst of pre-season training and the A-League doesn't kick off until mid October.
City are out of the Australia Cup with Wong and Memeti both playing in the club's round-of-16 exit to part-time side Queensland Lions a fortnight ago.
Tatu, meanwhile, was part of an Adelaide youth side that took part in the Otten Innovation Cup in the Netherlands last week, even scoring against Manchester United.
Whether it is each player's load management or if their clubs feel they will be better served remaining on home soil, the trio's withdrawal has re-opened an issue that is continuing to cause Football Australia (FA) headaches.
Under FIFA and AFC rules, clubs are compelled to release players for national team selection if it falls in a designated international window.
But the under-20 qualification tournament is outside an international window, meaning clubs are under no obligation to let players join national team camps.
As part of A-Leagues clubs unbundling from FA in 2020, a five-year agreement was in place which allowed national team coaches to pick domestic players outside of an internationals window.
But that arrangement has since lapsed, leaving FA powerless and completely at the whims of clubs.
The issue reared its head in January earlier this year when a swathe of players were withdrawn from the Olyroos under-23 Asian Cup campaign.
Australia was knocked out at the quarter-final stage and coach Tony Vidmar later stood down.
Neither Adelaide or Melbourne City were available for comment to explain their respective players' absences.
Adelaide did, however, allow Feyzo Kasumovic to accept a call-up on Friday as part of four new additions to the Young Socceroos squad.
Western Sydney's Emile Katrib and Melbourne Victory duo Michael Ghossaini and Oliver Dragicevic were also added to Trevor Morgan's squad.