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.
"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.
"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.
