The decision could have huge ramifications on Capital Football's National Premier League, with the program's closure in August coming before the finals series.

It means the third-placed team in Capital Football's top competition could be ripped out on the eve of the finals.

The 10-team competition will also be forced to introduce a bye from next season onwards, while it also leaves a hole in the National Youth League.

Capital Football were contacted for comment but did not return phone calls, leaving questions about the future of the competition to simmer.

The Centre of Excellence squad playing in the NPL has divided opinion in the past and there are fears the FFA is relying on A-League club academies that aren't yet up to scratch to develop players.

FFA chief executive David Gallop said the Centre of Excellence "has served Australian football well over a long period but the time has come for change".

An FFA statement read the program caters to "a maximum of 24 boys" in the under 16 and 17 age groups and costs $1.6 million per year.

However Centre of Excellence coach Tony Vidmar said the fact "80 players" came through camps in the last intake has been neglected.

The FFA are working to establish A-League and W-League club-based academies, but just days ago Vidmar said those programs would not be ready for some time.

"We believe FFA resources can be better used in a decentralised and expanded system that provides opportunities for many more young male and female players within club settings around Australia," Gallop said in a statement.

"The reality is that increasingly, some talented young players are choosing to stay with their local clubs or find places in Hyundai A-League academies and our schools program.

"Even among those who have attended the Centre of Excellence in recent years, fewer than half have gone on to become professional players.

"We are working with clubs and member federations to create a player development system that will be able to grow with the game around the country, recognises the evolution of Hyundai A-League and Westfield W-League clubs and their academies and meets the requirements of our national junior teams programs."

It's a stark contrast to years gone by, with the decision to lock the Centre of Excellence gates bringing an end to the program that bore Australian soccer's golden generation.

The likes of Ned Zelic, Craig Moore, Brett Emerton, Lucas Neill, Mark Viduka, John Aloisi, Mark Bresciano, and Vince Grella all came through the program - many of whom played a key role in Australia's rise up the world rankings.

The Centre of Excellence's five staff members and 20 current scholarship holders were informed of the decision on Wednesday afternoon.

Players will be given the option of staying in Canberra to see out the school year, while staff arrangements are being discussed on a case-by-case basis.