He has named several players with problems in his preliminary 24-man squad, including Charles Kaboré, Préjuce Nakoulma, Jonathan Pitroipa and Bertrand Traoré.
"I am confident they can recover in time," Duarte insisted.
The squad is due to begin a training camp on 27 December.
Bakary Koné is another player from the 2013 squad that finished as runners-up in South Africa who has an injury concern.
Injury has ruled out Aziz Kabore, who plays for Valenciennes in France, while there is a first call-up for Blati Toure.
The 22-year-old was born in Ivory Coast, played as a junior in Spain but is now at Omonia Nicosia of Cyprus.
"Blati Touré is a player I adore. I've watched him since he was at Evian TG I France but I was told he was Ivorian, but he called me to assure me he is 100 percent Burkinabe," Duarte explained.
"He hasn't yet trained with us but he is player with the quality to make a positive addition."
Also included are the uncapped Morocco-based Ernest Aboubacar Congo, called up last month for the first time for last month's World Cup qualifier against the Cape Verde Islands, and Issoumaila Lingane of Hapoel Ashkelon in Israel.
Besides Aziz Kabore, the most significant absence is first choice goalkeeper Daouda Diakite, who was seriously injured three months ago playing for AS Vita Club in the Democratic Republic of Congo.
The Stallions will leave Ouagadougou on 27 December to train in Marrakech where they play a Morocco B team on 4 January and Mali a few days later.
Burkina Faso meet Cameroon in Libreville in their first Group A game on the opening day of the Nations Cup finals on 14 January.
Squad:
Goalkeepers: Germain Sanou (Beauvais, France), Hervé Koffi (ASEC Abidjan, Cote d'Ivoire), Aboubacar Sawadogo (RC Kadiogo)
Defenders: Ernest Aboubacar Congo (IZK Khemisset, Morocco), Yacouba Coulibaly (RC Kadiogo), Youssoufou Dayo (RCB Berkane, Morocco), Bakary Koné (Malaga, Spain), Patrick Malo (Smouha, Egypt), Issouf Paro (Santos, South Africa), Steeve Yago (Toulouse, France)
Midfielders: Cyrille Bayala (Sheriff Tiraspol, Moldova), Adama Guira (Racing Lens, France), Charles Kaboré (FC Krasnodar, Russia), Prejuce Nakoulma (Kayserispor, Turkey), Jonathan Pitroipa (Al Nasr, United Arab Emirates), Bakary Sare (Moreirense, Portugal), Blati Toure (Omonia Nicosia, Cyprus), Abdou Razack Traore (Karabukspor, Turkey), Alain Traore (Kayserispor, Turkey), Jonathan Zongo (Almeria, Spain)
Forwards: Aristide Bance (Asec Mimosas, Ivory Coast), Banou Diawara (Smouha, Egypt), Issoumaila Lingane (Hapoel Ashkelon, Israel), Bertrand Traore (Ajax Amsterdam, Netherlands).
Burkina Faso coach Paulo Duarte says he has is not concerned over a number of injuries to key players going into next month's African Nations Cup finals.