FIFPro said in a statement on Tuesday that French striker Moukwelle Ebanga Sylvain, who played for the Indonesian Premier League club Persewangi Banywangi, had not been paid for nine months and had suffered typhoid and stress.
Moukwelle's plight follows that of Paraguayan Diego Mendieta, who died of a treatable viral infection last month after going four months without being paid.
FIFPro lamented the Indonesia Football Association for their mismanagement in allowing the 32-year-old to die.
"It is unbelievable that a few weeks after the passing of Diego Mendieta, we are informed about another player in Indonesia seriously suffering from an illness and waiting in vain for the payment of his salary," FIFPro Division Asia/Oceania chairman Brendan Schwab said.
"Fortunately, Moukwelle has recovered from his sickness. But it is another warning sign that drastic reforms are needed in Indonesia."
Local media reports said Moukwelle was owed 237,000,000 rupiah (£15,500) by the club. FIFPro said the player had agreed to accept a reduced amount earlier this month but was still waiting for it despite assurances from Persewangi management.
FIFPro said that the professional footballers' associations of Indonesia and France had been working with Moukwelle and the club to try and resolve the issue, with the player refusing to leave Indonesia until it is resolved.
Accusations of mismanagement in Indonesian football have been long cast. Despite a huge population and widespread love of the game, the country continues to languish in the doldrums of world football and are ranked a lowly 156th by FIFA.
A continued power struggle between the PSSI and the rival KPSI is to blame and has resulted in two domestic leagues and at one point, two national teams.
FIFA have spent more than two years threatening to ban Indonesia but still the issues remain unresolved as the world governing body give them a stay of execution time and again.
The latest deadline to resolve the arguments is March 20 with the national team due to begin their Asian Cup qualifying campaign next month without a number of players they had chosen because of their affiliation to the rival league.
For FIFPro, enough is enough.
"FIFPro wants to reiterate that the Indonesian authorities must take their responsibility to act swiftly," the statement said.
"FIFPro does not want to report on any more professional footballers being victimized due to a lack of respect and/or effort of Indonesian clubs and authorities."