FA chairman Lord Triesman admitted the collapse of Setanta which left the FA facing a £70m cash shortfall, had hindered the project but Watmore said Burton "has not been put on a backburner".
"There remains a strong commitment within the organisation to get the centre up and running," said Watmore.
"However, the project has to be financially sustainable."
Plans for the Burton centre, inspired by France's successful academy at Clairefontaine, were first unveiled in 2001 but were delayed for a number of years during the construction of the new Wembley stadium.
The hold ups culminated in a decision to halt construction in 2004 with only the basic infrastructure and pitches completed.
Setanta, who screened England's away World Cup qualifiers and FA Cup games, went into administration in June 2009.
It also had a contract with the FA to broadcast England's home friendly matches, England Under-21 games and the FA Community Shield.
The broadcaster failed to make a number of payments to sporting organisations, including the Scottish Premier League.
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