Charles Bakkabulindi, the Ugandan State Minister for Sports, has warned the national football federation that the government will be unwilling to pay the salary of the new head coach unless they are involved in his appointment.
The Cranes opened the recruitment process to find a long-term successor for Milutin Sredojevic on October 23, with the new head coach expected to be revealed on November 15.
However, Bakkabulindi has told KweséESPN that the government must be involved in the selection process if FUFA are expecting them to foot the bill for the new national team manager.
"There is no way the FA will get a new coach and expect the government to pay the salary when government is not involved in the recruitment process from the start," Bakkabulindi began.
"I do not want a scenario where the FA will appoint a coach and simply tell us we are meant to cater for certain amount of money when we the government were not in the negotiating process to also discuss the salary issue," he added.
Serbian coach Micho ended Uganda's near four-decade absence from the Africa Cup of Nations with qualification to the continental showpiece in Gabon earlier this year, but left the post two posts due to salary arrears.
Claude Le Roy is the most high-profile coach to have been linked with the post, and would bring considerable experience to the Cranes job, having guided Cameroon to the 1988 Nations Cup title.
He also enjoyed stints with Senegal, Ghana, Congo-Brazzaville and the Democratic Republic of Congo among others.
Former Uganda boss Bobby Williamson has also applied for the post, while Jackson Mayanja and the Cranes' interim head coach Moses Basena are two local candidates.
Speaking in response to Bakkabulindi, Uganda FA's Chief Executive Officer Edgar Watson told KweséESPN that the government were already represented on the vetting panel.
"By having a member from [the National Council of Sports], the government is catered [for] in the recruitment process," explained Watson, with the NCS being the government body that runs the nation's sport.
The FA's CEO, however, refused to clarify whether the government would be involved in the new head coach's salary negotiations.
CAF technical committee chairman and former Zambia FA President Kalusha Bwalya is the head of the committee that will vet the coaches who applied for the job, before the FA's Executive Committee make the final decision on the new appointment.
The new coach will be expected to start his tenure during the regional 2017 Cecafa Senior Challenge Cup which will take place November 25 to December 9th in Kenya. Uganda Cranes are the defending champions of the regional Championship.