The 32-year-old striker, married with two children, died late on Monday in a hospital in Solo, Central Java, the Jakarta Globe reported.
The paper said Mendieta, who had also played in China and Malaysia, had wanted to return home but was unable to do so as the club owed him four months' wages worth 120 million rupiahs (£7,764).
"He always complained of being lonely," Guntur Hernawan, the head of the internal medicine division at Moewardi Hospital in Solo, told reporters on Tuesday. "He said he wanted to go home because all of his relatives were in Paraguay."
Former Persis manager Totok Supriyanto was quoted by the paper as saying the outstanding debt would be paid to Mendieta's family.
Solo mayor Hadi Rudyatmo said would he personally pay the player's hospital bills and other expenses but called on others to help.
FIFPro described the case as a disgrace.
"FIFPro demands that the Indonesian football association make an end to the structural mismanagement of countless football clubs," it said in a statement.
"It is a disgrace for the whole of professional football in Indonesia," added Frederique Winia, secretary general of FIFPro's Asia division.
"I know countless stories of players who are intentionally not paid by their club and have to wait for months for their salary. But I have never before heard a story where a seriously ill player has been left completely to his fate by a club.
"I assume that both the club and the national football association of Indonesia realise that they have seriously failed and that they have much to explain, particularly to the family and relatives of Diego Mendieta.
"The least the club can do is to pay the arrears in salary to his family."
Mendieta's wife Valeria said she had been promised that she would receive the outstanding wages.
"He was practically abandoned, the only help he received was from three Paraguayan companions, nothing other than that," she told Radio Cardinal in Asuncion.
- Sports & Recreation