The Aussie is in despair at the sight of Fulham at the bottom of the table and looking strong favourites to be relegated after 13 years in the top flight.
Schwarzer told the London Evening Standard: "I think a lot of people underestimated the nous that Mr Fayed had in running a football club and knowing what it takes to stay in the Premier League, what decisions to make in terms of personnel, players, coaches and everything else. He had football directors alongside him and they ran the club very, very well.
"A new guy has come in and bought the club with no experience in football whatsoever and is relying on other people to give him advice. Unfortunately for the club it hasn't worked. This season has turned out to be a disaster.
"Hindsight is a wonderful thing. When someone goes, people do think maybe it's great to have a change and have another chairman come in with a lot of ambition. But what Mr Fayed did for the club was truly remarkable when you think about where they came from when he took over [they were in what is now League Two] to establish themselves as a top-flight team for over 10 years.
Mistakes: Schwarzer believes that Shahid Khan has made errors "This season there has been three managers and again that has a lot to do with the advice the chairman is getting. If you look at it, Mr Fayed and his board of directors were very astute, calm and knew what they were doing when it came to running a football club. It's obvious to me that at the moment they are lacking in direction and knowing who is really making decisions."
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