World governing body Fifa says a ban "may have to be imposed on" Zimbabwe unless the elected FA regains control of the sport by 3 January.
Last month, the Zimbabwe FA (Zifa) board was suspended by the Sports and Recreation Commission (SRC), a body mandated to develop sport by the government.
Fifa disapproves of governmental interference in the running of member associations and has banned countries from all forms of football as a result in the past.
The warning puts Zimbabwe's participation in next month's Africa Cup of Nations, which runs from 9 January to 6 February in Cameroon, into doubt.
The SRC informed Fifa last week that it had appointed a nine-member "restructuring committee" which could be in place until December 2022.
SRC chair Gerald Mlotshwa has previously said his organisation is willing to risk a ban if that is what is required to clean up Zimbabwean football.
The reasons given for the SRC's intervention include mismanagement and lack of accountability by Zifa in its use of public funds as well as alleged sexual harassment of female referees.
"If we are suspended from Afcon, we are prepared for that - that is fine," Mlotshwa said in mid-November. "Zimbabwean football needs this opportunity just to fix itself."
In the event that SRC does not relinquish control by 3 January, Group B at next month's Nations Cup could feature three teams - Guinea, Malawi and Senegal - should Zimbabwe be banned.
"Appropriate sanctions may have to be imposed on Zifa," warned Fifa's letter dated 21 December.
"In such a case, all of Zimbabwean football would suffer the consequences, especially on the eve of the Africa Cup of Nations.
"It is up to Fifa alone to remove executive bodies of member associations and appoint normalisation committees."
Last month, football's world governing body appointed normalisation committees to run football in Chad and Guinea.
A statement from the Zifa board on Tuesday said it had forwarded Fifa's correspondence to the SRC.
Coaching appointment called into question
The dispute between Zifa and the SRC has already impacted Zimbabwe's preparations for the Nations Cup.
Earlier this month, the secretariat running Zifa's affairs announced that Norman Mapeza will coach the side in Cameroon, following guidance from the SRC.
However, the following day, a statement from the suspended Zifa board called this into question, saying: "The board has not appointed any national team coach."
It added that the SRC had "illegally usurped" their powers by "clandestinely assuming the role of an interim committee".
Zimbabwe's technical team named a 30-man preliminary squad for the tournament on Tuesday.
The Warriors will be without influential midfielder Marvelous Nakamba after the Aston Villa player had surgery on a knee injury.
Zimbabwe has been drawn in Group B alongside Senegal, Guinea and Malawi.
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