The Uruguayan frontman has been recognised by both the Professional Footballers' Association and the Football Writers' Association after scoring 31 goals in 32 Premier League appearances for the Anfield outfit this season.
However, Chelsea manager Mourinho believes the awards should always go to a player from the league winners and suggested Dzeko would have been a more deserving recipient with City on the brink of the title.
"Luis Suarez is a very good player," he is quoted as saying in the British press. "They're not voting for a player who has no quality.
"(But) the profile of a player who wins the player of the year is not the profile of player who used to win in English football 10, eight, six years ago.
"He bit (Chelsea's Branislav Ivanovic) not this season but the previous season. This is a different season. I'm not speaking about one mistake that a man can have. You don't have to be punished for the rest of your life if you make a mistake on the football pitch.
"(But) my player of the year would be always from the champions, in every condition.
"If the champion is Man City - they need a point - I would say a Man City player and if I have to choose one, I would choose Dzeko.
"The kind of player he is, he's not just a goalscorer. He assists, he plays, he behaves, he's fair, doesn't dive, doesn't try to put opponents in the stands with accumulation of cards.
"He was the third (choice) striker at the beginning of the season. He was hidden behind his manager's first choices and when the team needed him in crucial moments of the season, I think he made the difference.
"In this moment I think he has 16 goals. Sixteen goals for the third striker is something spectacular."
Dzeko's 16 goals have come in 30 league appearances for City.
