Scudamore is calling for change at the top of the organisation and expects president Sepp Blatter not to make a U-turn on his decision to resign.
He told Sky Sports News HQ: “You sit there with some despair really because it is the game you love and the idea that the world governing body is going through such turmoil.
“Obviously this is an investigation and we can’t run too far with it at the moment, but clearly it looks like there has things been going on that are just wholly unacceptable.
“It’s the accountability really, who is holding this organisation to account and things have got to change.
“We know things have got to change and let’s just hope that the people who are charged with the responsibility of that – and it’s not us, we don’t have a vote, the Premier League, obviously our own Football Association does – but let’s hope that the changes can be made to bring some sort of respect and credibility back to the game because it’s a way of operating that we just don’t recognise.
“The way we govern the money in the game within the Premier League is so different and we get very frustrated that we are somehow associated with things that are done in a very different way.”
On Blatter’s future, Scudamore added: “I’ve only seen the media coverage that has been given but I did see his press conference and to me he had resigned and that means he is going.”
Meanwhile, Scudamore says he has no issue with more foreign owners buying clubs in the Premier League.
West Brom are the latest club to become the subject of a takeover and hope to have new owners by the end of the month.
Scudamore said: “We are open to the world, the top talent can come here and we are so successful in terms of the way the whole world wants to watch us, it’s inevitable therefore that people are going to want to come from all over the world to own our clubs.
“The only thing that really matters is: are they good owners, do they pass all the required tests, do they pass all the required financial rules now – much, much tighter rules than we have ever had before in terms of sustainability, source of funds, where is the money coming from, it’s a complicated process.
“It takes weeks and weeks and weeks to get through our processes to make sure everything is in order. That’s all that matters to us and then when they come, that they are good owners and they abide by the rules.”