Over 1,000 deaths have been recorded as the virus sweeps through West African countries, with Guinea, Liberia and Sierra Leone badly affected.
And African football's governing body has ruled that nations where the outbreak is at its worst will not be able to host qualifiers scheduled for September.
A circular, signed by secretary general Hicham El Amrani and sent to all 54 CAF affiliated national associations reads: "CAF will maintain its schedule of matches on the entire continent, except for 3 countries: Guinea, Liberia, and Sierra Leone, which have recorded a great number of cases.
"CAF has decided to ask the three federations to relocate to a neutral country the matches of their teams participating in CAF competitions, for a period up to mid-September 2014."
However, the Rwanda Football Federation (FERWAFA) has also expressed concerns regarding their fixture against Nigeria in Calabar on September 6, after the continent's most populous nation also reported cases of the deadly virus.
"We wrote a letter to the Confederation of African Football for their advice on the situation in Nigeria," FERWAFA president Vincent Nzamwita said.
"We're waiting to see if they can change the game, it's a big worry."
He added that the federation is taking direction from the government of Rwanda.
"If the government decide that the Amavubi does not travel, then we shall respect that," he said.
So far CAF have only officially sanctioned two qualifiers to be played on neutral grounds due to the outbreak: Guinea v Togo on September 5 and Sierra-Leone v DR Congo on September 10.
The continental body said it took its decision based on "advice from several medical experts on the potential impact of the spread of the Ebola virus in relation to the organisation of matches and CAF competitions" and added that they had received a formal notice from the World Health Organisation (WHO) advising "an avoidance of huge gatherings that could facilitate the spread of the Ebola virus."
CAF promised to reassess the situation in mid-September 2014 and went on to state: "In addition, according to the same WHO recommendations, it is extremely important that every Federation, whose country is affected by the virus, should ensure that their respective delegations travelling abroad can be examined before their departure in order to ensure that no member can transmit Ebola.
"On the other hand, each National Association receiving delegations is obliged to communicate all the necessary information delivered by health authorities to ensure the reception of teams and officials from various countries, including those from affected countries, and to proceed, if necessary, to additional checks at arrival points if required."
