Indonesia dodged a ban after emergency talks involving the world governing body and Asian Football Confederation officials, FIFA president Sepp Blatter said.
"I think it was quite a Christmas or end of year gift to Indonesia that they haven't been suspended," Blatter said after FIFA's executive committee meeting in Tokyo.
FIFA had given the country's football association (PSSI) until December 10 to end a bitter row with the breakaway Indonesian Super League, following a previous deadline back in March.
"But now they have to work. Because something is wrong," added Blatter, who was in favour of banning Indonesia for their failure to bring the feud to a halt.
The rivals factions signed a memorandum of understanding in June agreeing to bring both leagues together but were forced to set up a task-force as yet another deadline passed.
The deadlock prompted intervention from exasperated government officials in a bid to restore order and Blatter made no bones about the fact Indonesia was walking a tightrope.
"It was time in my opinion to say 'stop it now' but the executive committee was of the opinion to give them three more months," the FIFA boss said.
"Can you imagine that in Indonesia they have two groups directing football, they have a good league but the players of that league can't play in the national team?
"They have submitted a road map and they have been given until the next FIFA executive committee meeting on March 20-21 next year to bring its house in order."
Indonesia faces being booted out of all international competition, its referees also becoming ineligible, while FIFA would also cut funding to the PSSI.
"FIFA's financial assistance will also be stopped," Blatter confirmed. "We hope that this decision must not be taken because a suspension is always very detrimental.
"Now everybody is keen to stop it now. They have had three years to do it, we will give them three months more."
A ban would jeopardise Indonesia's participation in the qualifying tournament for the 2015 Asian Cup which begins in February.
Indonesia soccer has lurched from one crisis to another, their 10-0 humiliation by Bahrain in a World Cup qualifier in February triggering a FIFA investigation.
The PSSI have tested FIFA's patience to the limit over recent years for poor management, political intervention and allegations of corruption.
"The road map is very easy," added Blatter on the eve of Sunday's Club World Cup final in Yokohama.
"They have to put their house in order, their statutes in order. Indonesia is a country of more the 200 million people.
"We are not here to stop national associations to play football. They have one last chance of three months to come back.
"We are here to help them. I'm sure they will do it. If they don't they will face the consequences."