"For more than two years, enormous chaos has ruled in Indonesian professional football. There are two rival football associations, two professional leagues and even two national teams," said FIFPro in a statement.
"Above all, there is a horrifying number of professional footballers who have not received any salary from their club for months on end."
FIFPro said it had written to FIFA president Sepp Blatter "to express the concerns of the World Players' Union and to support the widow of Diego Mendieta."
Mendieta, 32 and married with two children, died in hospital in December. He had wanted to return home but had been unable to do so because he was owed four months' wages by the Persis Solo club.
In January, FIFPro said French striker Moukwelle Ebanga Sylvain, who played for Indonesian Premier League club Persewangi Banywangi, had not been paid for nine months and had suffered with typhoid and stress. He later recovered.
"It is now March and nothing has changed in Indonesia," said FIFPro. "Clubs are still neglecting to pay their players the salary they have earned. The club Persis Solo has not even been punished.
"FIFPro urges FIFA and president Blatter to intervene decisively in Indonesia. How long must people wait? Must another player die before anything happens?"
Indonesian soccer has been ripped apart by the fighting between the country's football association (PSSI) and the Indonesian Soccer Rescue Committee (KPSI) which resulted in the populous southeast Asian nation having two domestic leagues and two national teams.
FIFA has long threatened Indonesia with punishments and bans if the row was not resolved with the latest deadline being extended to March 20.
The rival factions have agreed to hold a FIFA-requested joint congress in Jakarta on March 17 to try to move forward as one.
Indonesia performed pitifully in the 2014 World Cup qualifiers, losing all six matches in third round Group E of the Asian region. Results included a 4-0 loss to Qatar and 10-0 defeat by Bahrain.
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