The Confederation of African Football has decided to seed South Africa and Egypt who were champions in 1996 and 1998 respectively.
Mali and Cameroon take the other two top seedings as hosts and titleholders.
It means that the Super Eagles, who were champions in 1980 and 1994, will now play in a group as second best to either the hosts Mali, Cameroon, South Africa or Egypt.
It could also see a replay of last year's final between Nigerian and Cameroon taking place in the first round.
Nigeria are placed in the second tier of teams and it is possible they could be put with George Weah's Liberia and Bafana Bafana - and that means grudge matches.
Nigeria and Liberia were engaged in a fierce battle for a place in the 2002 World Cup including a war of words between George Weah and his Nigerian counterparts.
Score to settle
South Africa and Nigeria clashes still have an edge after the Super Eagles pulled out of the 1996 Nations Cup when Pretoria backed sanctions against former military ruler Sani Abacha.
Bafana Bafana won the Nations Cup, though many thought it was because Nigeria were absent - an issue which leaves the score unsettled.
Caf said the criteria for the 2002 Nations Cup were based on the performances of the teams in the last three Nations Cup finals from 1996.
The format also demoted four-time champions Ghana into the second tier of seeds together with two times champions DR Congo.
Tunisia, who have never won the Nations Cup are also in the second tier, ahead of Algeria, Ivory Coast and Morocco who have lifted the trophy.
Caf will approve its seedings on 6 September in Bamako before the draws are held.
Seeding list
1. Mali, Cameroon, South Africa, Egypt
2. Tunisia, Nigeria, DR Congo, Ghana
3. B. Faso, Algeria, Zambia, Cote d'Ivoire
4. Morocco, Senegal, Togo, Liberia