The Football Association has been strongly criticised by the government for failing to implement promised reforms, BBC Sport can reveal.
Sports Minister Gerry Sutcliffe has written to the heads of the FA, Premier League and Football League, questioning their ability to work together.
Sutcliffe expresses disappointment at the FA's apparent lack of development in crucial areas of the national game.
The FA has said this response poses "important challenges to the game".
The government's criticism stems in part from the FA's lack of progress on implementing in full the recommendations of the 2005 Burns report.
Lord Burns was asked to conduct a thorough review of English football's governing body with the aim of making it a stronger, more transparent organisation.
The issues raised by the original questions and the Minister's response represent important challenges to the game at all levels
Football Association statement
BBC Radio 5 live sports news correspondent Gordon Farquhar said: "The message from government is the national team may be riding high, but English football's governing body is not.
"The letter describes the FA's contribution to the recent government request for answers to seven challenges facing the game as disappointing and lacking substance.
"It says the FA must introduce two independent directors to their main board, and highlights shortcomings in advancing the women's game, planning for youth development, coaching standards and leadership.
"Any praise is largely reserved for the professional leagues, particularly over tougher rules for financial stability, and homegrown player quotas."
Asked for a response, the FA told the BBC: "We are looking forward to receiving the letter and studying it carefully.
"The issues raised by the original questions and the Minister's response represent important challenges to the game at all levels.
"They merit careful thought and a proper response with football working together in partnership."
Speaking on BBC Radio Four's Today programme on Thursday, Sutcliffe said his letter to the FA, Premier League and Football League was prompted by an uncoordinated approach from the three bodies to answering a series of questions put to them last year by the-then Culture Secretary Andy Burnham.
And he warned the government might consider withdrawing its £25m grassroots investment in football if the FA fails to address its concerns.
"That's one of the levers we have," he admitted. "It would be a last resort, and we certainly wouldn't want to do anything that would harm grassroots football.
"We will wait to see what the FA's response is to the letter that we put forward."
Sutcliffe denied the government's criticisms could threaten the FA's bid to host the 2018 World Cup finals.
"No, definitely not. At the start of the letter it says English football is a success story," he said.
"But this is a conversation that has been had now for a number of years. It started off in 2005, all I'm doing is continuing the dialogue.
"The problem was we had three individual responses to the questions Andy Burnham put last year. I think that in itself shows that there needs to be a coming together on the key issues."
In a separate interview with The Guardian newspaper, Sutcliffe added: "There has to be, and there already is, a recognition that the status quo is not good enough.
"(The FA) must use this opportunity to put its house in order. If that doesn't happen the influence of the FA will diminish and football as a sport will suffer."
One of the areas highlighted by Sutcliffe is a lack of progress in developing the women's elite game, and Claire Wheatley, the development manager of Arsenal Ladies, backed his criticism.
She told BBC 5 live's Breakfast programme: "We need to make sure that there is a massive investment of capital behind the game, so we can have a real solid foundation of a good league.
"At the moment there are problems with facilities, games are often called off, so people won't generally come back if they've turned up and the game's off, and there's some real basic issues we need to deal with."
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