Watmore stepped down from a post he had held for less than a year after growing frustrated that his proposals for change were being blocked.

The FA will now search for a seventh chief executive in 10 years after naming Alex Horne to act in the role following an emergency board meeting this afternoon.

Mawhinney is well placed to speak on the FA's relationship with the professional leagues given his seven-year service to the Football League.

"There is no doubt that there is a structural problem, not least in the relationship between the FA on one hand and the two professional leagues on the other," the 69-year-old told Sky News.

"There may well be personality issues as well, but there is a structural problem.

"I suspect that what we are hearing is an implicit recognition that structural problems still exist."

FA chairman Lord Triesman tonight denied reports Watmore had left because of a personality clash and claimed there is stability at Wembley.

Mawhinney is not convinced, however, and added: "The FA board issued a statement tonight which says there wasn't a problem with the professional game, that there really wasn't a problem with any individual, that there isn't a problem that they can't solve and we don't need government to solve.

"So we're left asking, if that's the case, why did he go?"

Mawhinney does not believe Watmore's departure will have a negative effect on the national team or England's bid to host the 2018 World Cup.

"No I don't think it does," he said. "While it's not a good image to be projecting to the world of football, which tends to be a fairly closed world, is it going to affect Fabio (Capello)? No.

"Fabio is bigger and better than that. Fabio can deal with the players, he's demonstrated that.

"There was a separate company set up to handle the 2018 World Cup bid and it's working hard.

"So again I don't think the FA chief executive going makes a huge difference except to the extent it distracts and is not a great PR message."