The 51-year-old quit just 80 days before England’s World Cup bid amid reports he had become fed up with the on-going power struggle with the Premier League.
Watmore only undertook the role last summer after being appointed in February 2009 following the resignation of Brian Barwick. He is the sixth chief executive to quit in 10 years.
Although no reason has been given for Watmore’s departure, it is suggested he was frustrated by the power wielded by the Premier League in the governing body’s corporate structure.
It has also been rumoured that tensions have mounted between Watmore and FA chairman Lord Triesman in recent months, even though the pair had previously worked in the same government department.
Watmore was Triesman’s civil servant when the Labour peer was minister at the Department of Innovation, Universities and Skills, and some believe Triesman had struggled to adapt to Watmore making the step up to working alongside him.
Triesman, however, insists Watmore’s resignation was accepted “with great regret” and said he even asked the 51-year-old to re-consider his decision. In a statement, he 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’s brief stint in charge will be remembered largely for England’s impressive World Cup qualification campaign under Fabio Capello, while good progress was also made on the National Football Centre in Burton.