World football`s governing body said local authorities had intervened to undermine a committee appointed to run the game there following a serious corruption scandal.
The national team and all the country`s clubs will be excluded from all international competitions.
Senior Fifa official Primo Corvaro said the ban might not be immediate.
A former Fedefut president, Brayan Jimenez, pled guilty in July to racketeering charges after receiving hundreds of thousands of dollars in bribes to award lucrative marketing rights to his country`s World Cup qualifying matches to a Florida-based company.
After his arrest Fifa set up a committee to oversee Fedefut.
Sports regulators within Guatemala suspended the committee last week, saying it had not correctly used a procedure for looking into players who had been sanctioned for doping.
Mr Corvaro said this was unacceptable "interference".
"This means Fedefut will be isolated and will not be able to compete at international level," he said.
"It is a very serious situation. Financial support will end, as will training courses."
Mr Corvaro said Fedefut should expect a confirmation letter soon and the suspension would remain in place until the Fifa-run committee was allowed to operate again.
Guatemala`s national side has already been knocked out of the running for the 2018 World Cup but in the team`s last match, striker Carlos Ruiz became the highest-scoring player in World Cup qualifier history, scoring five goals to bring him to a total of 38.
Fifa to suspend Guatemala teams over `political interference`
16 September 2016
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The Guatemalan football federation, Fedefut, will be suspended by Fifa amid a row over political interference.
