The Stallions arrived at the Kruger Mpumalanga Airport yesterday afternoon only to find out that no arrangements had been made for their flight to Johannesburg, where they are supposed to train for the final against Nigeria.
The final takes place at the National Stadium.
The side spent hours at the airport after CAF promised to organise an alternative flight.
At the time of going to press last night, Joseph Mabhika, Local Organising Committee's delegate to the Burkinabe team, said: "We were promised that by 7.30pm there would be an aircraft here for us. It seemed they would organise a private jet, but we are still here and have had no feedback from CAF."
The team expressed concern that they would not get enough time to train ahead of Sunday's clash, having missed the chance to train yesterday.
"The entire team is here. The players are tired and we don't know when we will be able to leave for Johannesburg," said Mabhika. "This is unfair for the team and will make it very difficult to prepare for the important final."
This latest setback adds salt to injury for the Stallions following the controversial red card that was given to one of their star players, Jonathan Patroipa, in their semifinal victory against Ghana.
Burkina Faso have appealed the red card. Attempts to get confirmation on the decision of the appeal were unsuccessful at the time of going to press, but it is believed a decision will be made today.