Greg Clarke has "tarnished" his success in forcing through governance reforms at the Football Association with recent comments, according to sports minister Tracey Crouch.
Former basketball star John Amaechi, one of Britain's most high-profile gay athletes and now a leading psychologist, said on Friday that Football Association chairman Clarke visited his office in March to discuss how the FA could persuade gay male players to come out while still in the game.
Amaechi told him this was the wrong strategy and the FA needed to do much more to promote diversity and equality throughout the organisation but Clarke said that would get him the sack and the government would never intervene.
Speaking to reporters in London on Tuesday, Crouch said she was "not impressed" with these comments.
Asked if Clarke was right about the government not stepping in, she said he was "wrong" and, when pressed on what the government might do, she warned "he'll have to wait and see."
Until last week, the minister has been one of Clarke's biggest supporters, as he managed to persuade the FA to implement her new governance code -- a set of rules on decision-making and diversity all sports organisations in receipt of public money must meet by the end of this month.
For the FA, this meant bringing in term limits for its board and council, introducing more women and independent voices to both bodies and transferring more power from the council to the board.
Crouch has repeatedly praised Clarke for achieving this, as it had proved beyond his predecessors.
But she admitted: "In terms of what he and the FA have done in meeting all of the big headline issues of the code, this serves to tarnish that success."
On Amaechi's point about FA inaction on anti-gay sentiments, Crouch agreed, saying she has been asking the FA "to do more" for some time.
"Anybody involved in football should feel confident enough to be able to come out," she said.
Clarke's performance before the Digital, Culture, Media and Sport (DCMS) committee last week was described by one MP on the panel as "shambolic."
The committee summoned Clarke and three other FA bosses to explain their response to allegations of bullying and racism made against Mark Sampson, the former England women's team manager.