Pierre-Emerick Aubameyang says he was hurt after Yaya Toure said it was "indecent" to give the Gabon forward the African Player of the Year award.
Manchester City midfielder Toure said the decision had brought "shame" on the continent, while Swansea's Andre Ayew also questioned the move.
Ivory Coast's Toure and Ghana's Ayew reached the African Cup of Nations final, and Gabon went out early.
"I was hurt by what was said," Borussia Dortmund striker Aubameyang said.
"It's a shame."
In a vote of coaches and technical directors of Caf nations, Aubameyang got 143 points, with Toure on 136 and Swansea midfielder Ayew on 112.
Toure, BBC African footballer of the year for 2015, had won the Caf award in each of the previous four years.
"The award is based on the whole year and not just the African Cup of Nations," added Aubameyang, who is currently the leading scorer in the Bundesliga with 18 goals.