The Indonesian government insisted Wednesday it would stick by a decision to freeze all activities of the football association despite a threat from FIFA to suspend the country from international competition.
The sports ministry said it was only trying to make improvements and may dispatch a team to lobby FIFA president Sepp Blatter, after the governing body threatened to ban Indonesia unless it revoked its decision.
The FIFA warning was the latest twist in a row that erupted in April when the association, the PSSI, halted the country's top-flight league due to a disagreement with the sports ministry over the participation of two clubs.
The ministry then froze all activities of the PSSI, and said it was setting up a transitional body as a step towards replacing the association.
FIFA has backed the PSSI, which insists it remains in charge of football in Indonesia and that the the government has no authority on the matter.
It is just the latest crisis to hit Indonesian football, which has for years been beset by infighting and corruption. It was only just recovering from a feud between the PSSI and a breakaway association, which led to the creation of two separate leagues.
In a letter this week, FIFA secretary general Jerome Valcke said that Jakarta had to revoke its decision to freeze the activities of the PSSI by May 29.
Valcke said the government had violated FIFA rules that stipulated that all football associations have to manage their affairs independently, without influence from third parties.
If it refused to do, "we will have no other option but to refer this matter to the appropriate FIFA body for an immediate suspension", said the letter, which was widely cited in local media.
Sports ministry spokesman, Gatot Dewa Broto, told reporters that the government was "very anxious and very serious in overcoming this problem" and conceded a ban would mean Indonesia missing out on playing in competitions such as the Southeast Asian Games and the Asian Cup.
However he added that the effort to oust the PSSI was an attempt to improve the domestic game.
"This is part of making improvements. Just because the government has been threatened by FIFA, it does not want improvements which have been on the right track to slide backwards," he told reporters in Jakarta.
He added the government would send a reply to FIFA's letter in the coming days setting out their position, and if that failed to change the governing body's view, Indonesian officials would travel to Switzerland, where FIFA is headquartered, to meet Blatter.
The PSSI confirmed that the association had received the FIFA letter on Monday.
The row has caused anger among supporters in Indonesia, where football is wildly popular, with hundreds of fans staging a protest outside the presidential palace on Tuesday demanding President Joko Widodo intervene.
Despite the suspension, PSSI sought to restart the top-flight league, the Indonesian Super League, at the end of April but failed to do so after the police refused to issue match permits.
During the earlier row between PSSI and a rival association, FIFA also threatened to ban Indonesia from international football, but the two sides eventually resolved their differences and avoided sanctions.