Denis Obua has resigned as president of the Federation of Ugandan Football Associations (Fufa).
"I am out and will concentrate on my position as president of Cecafa," Obua told BBC Sport.
Obua said he was leaving the job because the government had made it impossible for him to carry out his duties.
The resignation comes after the government suspended Fufa on 2 February, amid allegations of corruption within the body.
The former Fufa president also said that he will withdraw the court case instituted against the government, to avoid a possible international ban from Fifa.
Jasper Aligawesa, secretary-general of Uganda's National Council of Sports, said the departure of Obua was in the best interests of the country.
"It is not that we don't like Obua but there should be some order," Aligawesa said.
The National Council of Sports has been in charge of football administration in the country since the government suspended Fufa.
Meanwhile, a Fifa delegation will visit the country between 6-8 March to assess the state of affairs in the country and chart a roapmap for the reorganisation of Fufa.
The decision was taken by the body's committee for national associations, which met in Zurich during the week.
"A normalization process will begin there," Fifa deputy general secretary Jerome Champagane told BBC Sport on Friday.
"After a delegation has visited the country, we should start a process and draw up a roadmap in order to change things there.
"It is likely that a normalisation committee will be set up for this process, which will involve the redrafting of the FA statutes and the organisation of regional and national elections," Champagne said.