The Mali Football Federation (FMF) has condemned the treatment of its squad and supporters during their recent qualifying trip to Benin.
It said players, officials, fans and reporters had been faced with "aggression and vandalism, before, during and after Sunday's match".
The game ended in a 1-1 draw - leaving both teams unable to qualify for the 2010 World Cup.
The FMF has asked for action to be taken against Benin.
Buses carrying Malian fans were attacked before the game.
Mali also say the playing squad and officials were attacked after a training session the day before the match.
Benin's Football Federation responded by claiming that the problems had been caused because Mali supporters failed to stick to a security plan.
"We deplore what happened," Malick Gomina, the vice-president of the Benin federation told the BBC.
"Unfortunately the Malian supporters chose their own itinerary and that's how they were faced with some Benin supporters."
He went on to claim that the trouble had its origins in the previous qualifying game between the two sides in Bamako.
The FMF said it thanked the government of Mali for its "prompt reaction and intervention" and appealed for calm from its fans.
Both sides have said they must talk to sort out the problems ahead of future games.
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