Gareth Southgate called the former Leicester man into the squad as a late replacement, only for him to reject the call, citing a lack of fitness.
Drinkwater has made just four appearances for the 'Blues' since joining the club on deadline day, with his early Chelsea career being blighted by a calf problem.
His decision to turn down England's call led to widespread criticism for Drinkwater, something that Conte feels is unfair and that could have been avoided if Southgate had contacted him to discuss the midfielder's avaialability.
"It's a pity that a player had to pay for this misunderstanding," said the Italian.
"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 per cent fit to go with the national team."