Speaking at a lunch at Wembley to mark his 10-year anniversary as president, the Duke of Cambridge said the FA was in danger of being "left behind".
"Our governance structure is in danger of falling short of modern standards of best practice," he said.
"As the country's national sport, we ought to be leading the way."
Prince William, who took over the presidency from his uncle, the Duke of York, appeared to publicly back outgoing chairman Greg Dyke's efforts to reform the FA Council by making it more representative and diverse.
"There is a wind of change blowing through global sporting governance and we need to ensure we do not get left behind," he told guests, many of whom were FA board members.
"I know the organisation is currently reviewing this issue and there is an opportunity to seize the initiative by the way in which we reform ourselves.
"This is an emotive issue, and it is one that you all have a stake in deciding."
The Football Association's governance structure is in need of reform, says the governing body's president Prince William.