New guidelines from the Confederation of African Football state matches will go ahead even with no fit goalkeepers.
Any nation unable to fulfill a fixture will forfeit the game two-nil.
There have already been Covid cases in a number of squads, including Egypt and Gabon.
One of those Gabon players is Arsenal striker Pierre-Emerick Aubameyang, who has contracted the virus.
Aubameyang, former Southampton midfielder Mario Lemina, and coach Anicet Yala returned positive lateral tests on arrival at Yaounde's airport in Cameroon.
Head coach Patrice Neveu told AFP that the trio are isolating in their hotel rooms and awaiting results of PCR tests.
The first game of the tournament took place on Sunday, as Cameroon faced Burkina Faso.
Two goals from former Porto striker Vincent Aboubakar meant the hosts come from behind to take all three points.
However, Burkina Faso were fortunate to still have 11 players on the pitch after just one minute of the opening game.
Just 40 seconds into the match, Steeve Yago went flying into a remarkable challenge with his studs in the air.
He made contact with the genitals of Cameroon's Martin Hongla, who cried out in pain and fell to the floor.
Somewhat surprisingly though, the referee only produced a yellow card for the challenge.