FA board members will hold an emergency meeting at noon following Watmore’s decision to quit after only nine months in the job.
Watmore is said to have become increasingly frustrated with some of his proposals being thwarted. It is understood he was also concerned that Premier League chairman Dave Richards was blocking him and the FA on several issues.
His decision to resign comes in a year that will see a decision on England’s bid to host the 2018 World Cup. It also comes soon after he announced a four-year plan to sort out the association’s finances after the demise of Setanta and the cost of repaying the loans for the rebuilding of Wembley.
English football’s governing body has also overhauled its sponsorship structure in a bid to boost commercial revenues, signing new deals with Fiat, Nivea, Telekom Malaysia, Mars, McDonalds and Carlsberg in recent months.
It also integrated its Wembley Stadium and FA businesses last year to form the FA Group in an attempt to leverage the potential of the Wembley and England brands.
Watmore, a former Accenture managing director and chief information officer in the cabinet office, is the fourth FA chief to quit in eight years. Previous chief executives include soon to be ITV chief executive Adam Crozier and Brian Barwick.
FA chairman Lord Triesman says he accepts Watmore’s resignation “with great regret”.