Fifa warned the Ugandan government against forcing the country's Football Association (Fufa) to register as a trustee, which Fifa says would be "considered as interference."
In a letter dated 17 June to both Fufa and the Ugandan government, Fifa warned of possible sanctions if the FA registers under the government's "Trustees Incorporation Act."
It comes after Uganda's government gave all Uganda's sporting Federations a deadline of June 30th to register.
But the Uganda FA has refused to abide by the order which came through Uganda's National Council of Sports (NCS), insisting that by doing so, it will go against Fifa rules.
Fifa have now responded with a warning to the government.
"Fifa points to the bold fact that any form of forced incorporation of Fufa under the Trustees Incorporation Act would be considered as interference in contravention to the Fifa Statutes" stated the letter which was signed by Fifa's Deputy Secretary General (Administration), Marco Villige.
The letter also highlighted the consequences of government interference in Fufa matters which it states "would consequently be brought to the attention of the relevant Fifa bodies to take appropriate measures against Fufa, including sanctions."
The Uganda FA President, Moses Magogo said although they remain a law abiding body in their country, they do not want to sign a document which will contravene with the statute of football's world body.
"Let the government accept to meet the Fifa people and discuss the way forward," Magogo told the BBC.
Any possible sanctions, which could involve a world ban, would hurt the Cranes who are on the brink of qualification for the 2017 Africa Cup of Nations. A victory over Comoros in September will take them to the finals in Gabon.
They are also the only nation in the Cecafa region still involved in the 2018 Fifa World Cup qualifiers.