FIFA has warned Uganda to avoid government interference in its football.
The FUFA is the latest African federation to be threatened with an international ban after Cameroon was suspended for nearly three weeks this month over government involvement.
FUFA chief executive Edgar Watson said on Tuesday that the world body had warned Uganda's government in a letter. Copies also were sent to FUFA and the Confederation of African Football.
A Ugandan government minister wants to reform some of FUFA's rules, while FUFA said FIFA's warning was "the climax" of a long-running feud between the federation and the government.
Any FIFA ban might affect Uganda's place in World Cup qualifying, where the East African nation must beat Senegal in September to make the final playoffs.
Cameroon's ban was lifted on Monday.