League officials said they would ignore the findings of BOPI's review of all 18 clubs, which delayed the season by six weeks while it was being conducted, and kick off as planned with the backing of the Football Association of Indonesia (PSSI).
However, BOPI officials, who also voiced concerns about the running of 11 other clubs in the troubled league, warned they could take the case to the courts if their recommendations were not followed.
A FIFA spokesperson told Reuters late on Thursday they were monitoring the case and said only the PSSI were the recognised body to govern the sport.
"We can confirm that a letter from FIFA Secretary General Jerome Valcke was sent on 19 February 2015 to the Football Association of Indonesia following the postponement of the start of the Indonesian Super League," the spokesperson said.
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"In the said letter, the Football Association of Indonesia was reminded that member associations must manage their affairs independently and without influence of any third parties as clearly stipulated in articles 13 and 17 of the FIFA Statutes."
Article 13 I asks member associations to stay independent, while 17.4 says FIFA will not recognise decisions made by bodies not elected by the local association.
BOPI's review came with the new government keen to repair football's tarnished image in the country after years of corruption and players going unpaid in the league, while a lengthy battle for power took place at the PSSI.
Paraguayan player Diego Mendieta, who had gone unpaid at his club for months and had no money to pay for his care, died in 2012, resulting in scathing criticism from world player's union FIFPro.
Last year's ISL was the first to run with some sort of cohesion after a merger with the rival Indonesian Premier League, suggesting things were moving on the right path.
Further promising signs came on Friday with the Qatar National Bank Group announcing a three-year title sponsorship of the league until 2017.
(Writing by Patrick Johnston in Singapore; Editing by Peter Rutherford)
