Pompey are being pursued by two Australian clubs for £360,000.
It is claimed the Blues owe the money following the transfers of six players, including Ryan Williams.
The debt dates from long before Pompey’s current financial problems but is another blow to the club as they face a winding-up petition by HMRC and the prospect of administration.
Williams was part of an Australian intake along with Alex Grant, Andy Higgins, Patrick Antelmi, Jordan Fitzharris and Billy Tsovolos.
Payments were due upon each player becoming a scholar, with a further sum to follow should they sign professional terms.
All have achieved that in the past 18 months – yet both ECU Joondalup and Blacktown City Demons have still to be paid.
It means Pompey have sold Williams to Fulham having not yet settled the development fee with the club from which he arrived at Fratton Park.
Both Joondalup and Blacktown have informed Football Federation Australia and indicated they would be willing to take their cases to FIFA for a resolution.
The Blues agreed to pay a total of £50,000 to Joondalup for Williams after he arrived in the summer of 2010.
The Perth-based club were scheduled to receive £20,000 in January 2011 and a further £30,000 in August 2011. Yet it is claimed nothing has so far been paid.
In addition, Joondalup are entitled to receive 20 per cent of Williams’ transfer to Fulham.
The News understands that transfer deadline day deal, negotiated by chief executive David Lampitt, was worth £295,000.
A sell-on clause was included, although there is believed to be no stipulation for future payments based on appearances.
Joondalup should collect £60,000 from that deal for the 18-year-old, taking the sum owed to them by Pompey to £110,000.
The Perth-based club are also due a total of £100,000 for fellow youngsters Grant and Higgins.
Central defender Grant is highly regarded by Pompey and has trained with the first team in recent weeks.
He has made 17 academy appearances this season – more starts than any other player – and has scored one goal.
Left-sided midfielder Higgins has also been a regular for Andy Awford’s side, with 12 starts and seven substitute appearances.
Blacktown City Demons are owed a reported £150,000 under terms of the transfers of Antelmi, Fitzharris and Tsovolos. Pompey apparently agreed to pay a total of £50,000 for each player upon them signing professional terms.
Tsovolos, who signed scholarship forms in July 2009, was released by Pompey this summer having failed to make the first team. He now plays for Eastleigh.
Antelmi is an Australian under-17 international striker who has scored two goals in eight games for the academy this season.
Utility player Fitzharris has made eight appearances.
Lampitt was unavailable for comment when contacted by The News.