Burkina Faso coach Paulo Duarte
The Portuguese's protest at competition organisers the Confederation of African Football (CAF) was made on Friday, 48 hours before they open their campaign against 2010 hosts Angola.
Duarte compared the treatment dished out to Burkina Faso with that received by his team's main first-round rivals, the Angolans and Nations Cup favourites Ivory Coast.
"They are protected. Everyone here is not working in the same conditions," he said.
"Some teams have journeys of 10 or 15 minutes to get to training, while we have to travel for one hour along a winding road to have a session (in Luba, 50 kilometres from their team hotel in Malabo)."
Duarte added: "When we arrived here, they gave us a restaurant/cafe to sleep in. It wasn't even a hotel. There was no video room, no conference room. Each time we have to improvise. That's what the Nations Cup is like."
Burkina Faso finally switched to more appropriate accommodation and chose a training ground situated adjacent to the stadium in Malabo.
Duarte's criticism triggered a forthright response from CAF.
General secretary Hicham El Amrani claimed the allocation of team hotels was conducted by lots "to avoid any injustice".
He added: "Burkina Faso's hotel was initially situated one or two kilometres from the training centre. If they had remained in the hotel which had been allocated to them, they would have been right beside the training ground."
Turning to matters on the pitch, Duarte described as "decisive" their curtain-raiser against Angola.
"We've inherited a difficult group with Ivory Coast and Angola. You can say that the Ivorians will qualify so this is a very important match for second place.
"The team which wins the first match will have done 80 percent of the work.
"But my problem is not our rivals, nor the group. We've had internal problems, too many regular players aren't here. (Midfielder) Alain Traore plays a specific role yet our attack is broken. We've turned up at 40 to 50 percent below our strength."
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