The club's chief executive believes that Ilkay Gundogan, Marcel Schmelzer and Mario Gotze expected to get more playing time for Germany at the tournament
Four members of the Bundesliga champions' squad travelled to Poland and Ukraine as part of Joachim Low's 23-man selection, but Mats Hummels was the only one to feature on a regular basis.
Mario Gotze played just 10 minutes in the tournament as a late substitute in the quarter-final win over Greece, while Ilkay Gundogan and Marcel Schmelzer failed to appear at all.
"I can understand that they are really frustrated, but I don't believe that Gundogan, Schmelzer and Gotze will be hung up about the Euros," Watzke told Bild.
"The three of them have strong character and will be very motivated after this experience."
Germany manager Joachim Low has come in for criticism following his side's semi-final loss to Italy, with many media sources questioning his decision to select Bayern Munich midfielder Toni Kroos in his starting line-up, but Watzke has defended the trainer's tactical choices.
"It is the privilege of the coach to select the team. Germany have so many great footballers, so it is normal that not everyone is satisfied with his decisions."