Both the Togo Football Federation (TFF) and the Sierra Leone Football Association (SLFA) have found their qualifiers in September are likely to be affected.
On Tuesday, the TFF announced it had received authorisation from CAF to play its upcoming qualifier against Guinea in a new venue.
This comes after Togolese officials approached the continental body saying its players were concerned about the outbreak of Ebola in Guinea and were concerned for their safety. More than 360 people have died in the country since the first virus infections were recorded in March.
In Sierra Leone last week, the SLFA suspended all football matches until further notice because of the outbreak. They also approached the Ghana Football Association (GFA) to play their home match against DR Congo on September 10 in Ghana.
Ghana FA spokesman Ibrahim Sane confirmed the approach, telling BBC Sport: "We have asked the Sierra Leone Football Association to use the government to contact our foreign ministry and ministry of health for clearances."
There could be more fixtures affected as Rwanda have also raised concerns over Ebola ahead of their scheduled trip to face Nigeria on September 6, after Africa's most populous nation confirmed they are dealing with 10 confirmed cases of the virus.
