FIFA has threatened to sanction Indonesia unless the football association (PSSI) restores order and unifies the rebel Indonesia Super League with the national league by March 20.
Government interference risks inflaming the situation still further.
But the National Sports Committee (KONI) has said it will take over the beleagured PSSI if it fails to end months of chaos by the weekend, the Jakarta Globe newspaper said.
"KONI is the sports authority in the country and we have a duty to make sure sports development, including football, runs smoothly," said chairman Tono Suratman.
"We've been encouraging the PSSI and KPSI to reconcile and work together to improve Indonesian football.
"However, if they fail to do that, we have to save the sport by taking over the PSSI."
The PSSI has been plagued by prolonged infighting and has been blamed for the national team's humiliating 10-0 defeat by Bahrain in their World Cup qualifier last month.
Indonesia were forced to field an inexperienced side after FIFA banned them from picking players from the rebel Indonesian Super League (ISL), which the PSSI has refused to recognise.
A reconciliation attempt between the warring factions on Wednesday drew a blank after only one club from the ISL turned up at a meeting at a Jakarta hotel.
PSSI deputy secretary general Hadiyandra warned of the possibility of sanctions if KONI went ahead with its plan.
"Even the president [Susilo Bambang Yudhoyono] knows the government cannot interfere with the PSSI because then the country would be suspended by FIFA," he said.
