After only making one start and three substitute outings for the Blues since a summer move, Drinkwater opted to work on his fitness with the Blues rather than feature for the Three Lions against Germany and Brazil.
However, Conte has defended the midfielder, claiming that Drinkwater was not fit and suggesting that the player's honesty should be 'appreciated'.
The 48-year-old told reporters: "It's a pity that a player had to pay for this misunderstanding. Drinkwater was very honest and he doesn't deserve to be attacked from the press or from the people because he was very honest.
"In this situation every single player wants to go with the national team. We have to appreciate his behaviour and commitment. If someone asks me I can explain. Before, to call [up] the player, if you call the coach [you ask] 'is this player good or does he have a problem? Is he tired or not?'
"In this way you can avoid a misunderstanding because, about Drinkwater it was a misunderstanding. He was injured and also he wasn't really 100% fit to go with the national team."
Drinkwater has returned to training ahead of Chelsea's Premier League meeting with West Bromwich Albion.