Messi overtook Ronaldo to become the first men's footballer to win the Ballon d'Or for a sixth time.
"The Ballon d'Or to Messi? For me it's an injustice," Mendes told Tuttosport at Monday's Golden Boy Award ceremony in Turin. "Cristiano is the best in the history of football. Before him Portugal had not won anything, with him the  European Championship and the Nations League.
"The Ballon d'Or? Had he played at Real [Madrid] he would have won it. He has transformed world football, in Portugal, at Real Madrid. It's impossible to compare him to anyone."
Messi scored 36 times last season en route to a 10th La Liga title, and was the Champions League top scorer. His goals in La Liga also made him the top scorer in Europe's biggest leagues, earning him the Golden Shoe award.
Ronaldo, who won four of his five Ballon d'Or awards while on the books of Real Madrid, joined Juventus in the summer of 2018 and helped the Bianconeri win their eighth straight Serie A title in his first season at the club.
He skipped the Ballon d'Or ceremony in Paris and instead attended the Gran Gala del Calcio in Milan to collect an award for the best striker in Serie A.
Ronaldo scored 28 goals in all competitions for Juventus, including 21 in the league. Missing out on the Ballon d'Or award has not distracted Ronaldo, according to Mendes.
"CR7 is a champion, who knows what to do and will continue to work," he said.