The Greece international has played just 30 minutes for Fulham since joining for a reported £12 million fee from Olympiacos on transfer deadline day, coming off the bench in last weekend's 1-1 draw at West Brom.
Magath - who will take charge of his first home match as Fulham boss on Saturday - confirmed the 25-year-old is not injured, but is still working towards full fitness so he can adapt to the physical demands of the Premier League.
"Mitroglou isn't ready at the moment but he's developing and I think next week [against Cardiff City] we can count on him, but the game against Chelsea is a bit too early," the German said.
"He doesn't have an injury, he has a lack of fitness. The Premier League is not the same as the Greek league.
"He's a very dangerous striker, sure, but in this league here you need to be fit to come into a situation where you can score and defend.
"We need him to be able to work hard for 90 minutes and at the moment he can't do that, but I'm convinced that he will belong to the squad next week."
Centre-back Fernando Amorebieta also misses out with a muscle injury, while Damien Duff will not face his former side due to a knock.
But, despite their absence, ex-Bayern Munich and Schalke boss Magath feels his team can upset the odds against Chelsea, as the Premier League leaders visit Craven Cottage just 72 hours after playing Galatasaray away in the UEFA Champions League last 16.
"It's always an advantage for teams when they play against a Champions League team and we're lucky that Chelsea had such a long trip to Istanbul," he added. "They played on Wednesday so it's a good situation for us.
"I remember those situations; you have to stay at the airport and fly a few hours, then you have the game at night, then usually the players cannot sleep and the next day you're tired.
"You're tired at the airport, you have to wait for the plane - I think it bothers the players a lot and for sure it's a chance for us. Chelsea are favourites but we've prepared for the situation and we try to fight and make it a fast game."