FIFA says the any imminent threat of Uganda being banned from global football for government interference has now been lifted.
The news comes after a meeting on Tuesday involving two representatives from football's world governing body.
A warning was issued in June when the Federation of Ugandan Football Associations (Fufa) was being asked to sign as a trustee with the government.
FIFA deemed this would be government interference which is prohibited under its statutes.
"We are happy the government has agreed not to interfere and will work for the development of football in the country," Luca Nicola, the Manager of Member Associations at Fifa said.
Nicola explained that all at the meeting had agreed the Uganda football association can indeed register as a trustee but that they had assurances from government that there will be no interference.
Uganda's minister for sports, Charles Bakkabulindi was also satisfied with the outcome of the meeting and added Fufa will now put it's paper work together and register as a trustee by next month.
Fufa president Moses Magogo was equally happy with the meeting and that a decision had been made that will meet FIFA's approval.
The Uganda national team will also be relieved as they can qualify for the 2017 Africa Cup of Nations finals in Gabon with a win over visiting Comoros in September.
The Cranes are also into the final round of qualifying for the 2018 World Cup.