A senior PSSI official told Thursday's Jakarta Post, football's governing body was unlikely to impose sanctions amid an embarrassing election crisis at the PSSI.
The PSSI's deputy secretary general Suryadharma Tahir said he had met FIFA officials after protests calling for current FA chief Nurdin Halid to be dismissed had turned violent.
The demonstrations followed last week's PSSI decision to prevent oil tycoon Arifin Panigoro and Army Chief of Staff General George Toisutta from standing against Nurdin.
The deeply unpopular Nurdin is seeking a third term as president.
Tahir said FIFA had called for the PSSI to put their house in order.
"I have told FIFA that the PSSI would repeat the selection process from the start," he told Metro TV.
"We have come to an understanding on this," he added, insisting FIFA would accordingly reject the option of punishing the PSSI.
The Indonesia government has been accused of interfering in PSSI business, something FIFA traditionally takes a dim view of.
According to Tahir, FIFA criticised Indonesian Youth and Sports Minister Andi Mallarangeng last week for "intervening" in the upcoming election.
Andi had condemned the PSSI for certifying only the application of Nurdin, who has thrown his hat into the ring for the 2011-15 term.
Angry Indonesian football fans have called for Nurdin to be ousted and he was summoned to the country's House of Representatives to answer charges of a lack of progress in his two terms in office.
Andi has said he was willing to speak to FIFA directly to clarify any perceived governmental meddling into PSSI affairs.
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