FA chief executive Watmore quits
In a statement on the FA website, chairman David Triesman said: "Ian Watmore tendered his resignation to me on Friday.
"I asked him to re-consider over the weekend. However, he has confirmed today that his position remains unchanged and I have accepted it with great regret.
"There will be a board meeting tomorrow at noon. I am unable to make any further comment until after that meeting."
Watmore worked for Triesman when he was minister for Innovation, Universities and Skills.
He had kept a relatively low profile since his appointment, but recently floated ideas to re-vamp the FA Cup in a bid to help the competition regain some of its former glory.
Recent media reports have hinted that problems have arisen between Watmore, a former civil servant who took over last June, and Triesman.
Watmore's departure is not expected to have an undue influence on the FA's bid to stage the 2018 or 2022 World Cup finals when the decision is made by FIFA in December.