The tournament starts on Sunday in the Ghanaian capital Accra, while Senegal play their opening Group D match against Tunisia on January 23 in Tamale. Bafana Bafana, who are in the same group, play Angola on the same day.
“The supporters will leave onboard the presidential plane which will do two trips to Ghana on the 21 and 22 of January," the ministry said in a statement.
With many ordinary Africans unable to afford airfares and road transport across West Africa dangerous because of poor routes and banditry, many fans risk missing the opportunity to see their sides in action.
Neighbouring Guinea has cancelled a convoy of buses supposed to ferry fans to Ghana because of concerns about road safety in war-divided northern Ivory Coast.
Senegal, who beat Benin 2-1 in a warm-up match on Wednesday, has set up a camp in Tamale to accommodate some 425 fans.
The Sports Ministry will provide some money for living expenses for Senegalese who travel to support the national team in Ghana.
Senegalese fans from Burkina Faso, Ivory Coast, Togo, Benin and Guinea Bissau are also set to benefit.