Mali missed out on a place in the last eight of the tournament in Equatorial Guinea after fortune favoured Guinea when lots were drawn on Thursday.
The two countries had finished with an identical record in Group D and so lots were drawn for the first time since 1988 to decide who will face Ghana in Sunday's quarter-final.
CAF media director Junior Binyam acknowledged that the regulation must be looked into ahead of future tournaments.
He is quoted as saying by BBC Sport: "We have to stand by the regulation but also think about how we improve it,
"It's not fair to have a team going out like this. It really is the worst decision - to have to make a decision this way - because everybody expected it would be decided on the field."
He added: "The decision of the agenda is not mine but I think it's a matter of concern for members of both the organising committee and the CAF executive committee,
"Regulations are not static, they are dynamic. We will find a way of improving the criteria to make them be decided by actions on the field.
"The situation that has happened in Group D will make people think twice,
"I am sure that in the weeks and months ahead, we [will make sure we] don't have the same situation in two years' time."
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