The warning came after an administrative court in the country issued a ruling on June 25 in favour of three local clubs who had complained about the election process in the Omani federation (OFA).
Oman, who have never qualified for a World Cup, have reached the fourth round of the Asian qualifying competition where they are fourth in Group B with two points from three games.
Coached by Frenchman Paul Le Guen, they progressed from their third round group at the expense of Saudi Arabia, recording a shock 1-0 win over Australia in the process.
FIFA said in a statement that enforcement of the court order would "allegedly entail the nullification of the said elections and the organisation of a new electoral process.
"All FIFA member associations have to manage their affairs independently and without influence of any third parties, as clearly stipulated in articles 13 and 17 of the FIFA statutes."
It added: "FIFA confirms that the OFA elections were held under the strict observation of FIFA and Asian Football Confederation (AFC) representatives and that those representatives duly asserted that the procedure of the election of the board of directors was carried out in accordance and conformity with the precepts of the OFA statutes."
It said that if the elections were annulled, FIFA would take measures "which could go as far as an immediate and indefinite suspension of the OFA."
"Such a suspension would jeopardise the participation of Oman in the 2014 World Cup qualifiers and other international competitions, and would also entail that neither the OFA nor any of its members or officials could benefit from any development programme, course, or training from FIFA or the AFC while the OFA is suspended."