Mitroglou has made just two appearances, including one start, since joining Fulham for a club record transfer fee in January, but has picked up a fresh knee injury this week.
"Dan Burn will miss the game, as well as Mitroglou," Magath told the club's official website. "Dejagah will be missing the game, also.
"Ashkan and Dan are muscle problems and Kostas has problems with his knee so the medical staff are working on it and we hope that he will be ready to play next week.
"It happened to [Mitroglou] last week so it's now a new injury. It's frustrating not only for the player but for us too because we are waiting for him and unfortunately we have to wait a few days longer. We hope that he will come next week to the squad and join us in the training sessions."
Fulham could move off the bottom of the Premier League table with a win over City.