The Duke of Cambridge has urged world football governing body Fifa to “show that it can represent the interests of fair play and put the sport first”.
Prince William, the president of the FA, made his comments during a speech before the cup final at Wembley.
He urged sponsors and other backers to use their influence with Fifa to support reform.
It comes after Fifa’s president Sepp Blatter was re-elected, following the arrests of seven people linked to Fifa.
The seven, arrested in Zurich earlier this week, are among 14 indicted on charges of bribery, racketeering and money-laundering, involving tens of millions of dollars since 1991.
Meanwhile, Swiss authorities have launched a separate criminal investigation into the awarding of the 2018 and 2022 World Cup tournaments to Russia and Qatar.
The prince led England’s bid team for the 2018 finals, which also included Prime Minister David Cameron and David Beckham among others.
In his speech at Wembley he compared the crisis engulfing Fifa to the Salt Lake City corruption scandal, which occurred when the US city was bidding to host the 2002 Olympic Winter Games, and it prompted the International Olympic Committee to reform.
He said: “There seems to be a huge disconnect between the sense of fair play that guides those playing and supporting the game, and the allegations of corruption that have long lingered around the management of the sport internationally.
“The events in Zurich this week represent Fifa’s Salt Lake City moment, when the International Olympic Committee (IOC) went through a similar period of serious allegations.
“Fifa, like the IOC, must now show that it can represent the interests of fair play and put the sport first.
“Those backing Fifa, such as sponsors and the regional confederations, must do their bit to press these reforms – we are doing football and its fans no favours if we do not.
“I have no doubt that when Fifa reforms, its mission to spread the benefits of the game to more people, especially those in developing countries, can only be enhanced.”
He also used his speech before match – which saw Arsenal beat Aston Villa 4-0 – to back a decision by former Manchester United chief executive and newly-elected Fifa vice-president David Gill to quit the position almost immediately in protest at Mr Blatter’s re-election.
Mr Blatter is not named in the indictment, and denies having anything to do with an alleged $10m (£6.5m) bribe.
Prince William said: “I know I join with all of you in commending David Gill for his decision to stand down from the ExCo [executive committee], and to lead by example by doing so.”