However, Capital Football believes it would be unfair to the remainder of the clubs in Canberra because they were unaware at the time a place in the ground-breaking nationwide tournament would be up for grabs.

A pre-season competition will be held in March and April featuring the eight teams in the Canberra National Premier League to determine who will represent the ACT in this year's FFA Cup.

The winner of Canberra's own knockout tournament, the Federation Cup, will qualify for the FFA Cup in subsequent years.

Thiele was adamant his club was entitled to secure the spot in the competition and have the chance to potentially take on the big guns from the A-League.

''The decision made this year not to allow the current Federation Cup winner to participate is incorrect and we don't understand Capital Football's reasoning behind it,'' Thiele said.

''It just defies all logic.

''I will write a letter with the expectation of the appropriate response from Capital Football and I don't see any reason why they shouldn't overturn it.''

The FFA Cup is a knockout competition based on the FA Cup in England and will involve 32 teams from across the country, including the nine Australian-based A-League clubs.

It is tentatively scheduled to kick off in late July, while the Federation Cup won't conclude until September.

It means clubs which only field teams in the second-tier Capital State League can't qualify for the FFA Cup.

''I was disappointed how this was outlined to the Capital Football clubs,'' Thiele said.

''The draw came out for the pre-season competition [in December] and it had in fine print the winner of this competition would go through to the FFA Cup.

''The FFA Cup was originally designed for a club at any level, so now they're going against what Football Federation Australia had originally established.''

Capital Football men's competition league manager Alasdair Grocock admitted the situation wasn't ideal, but said it was the fairest solution for the majority of clubs.

''At that stage the FFA hadn't decided how the mechanics of the FFA Cup were going to work,'' Grocock said.

''When we ran the competition last year, we weren't running it with any premise that the winner was going any further than being announced as the Federation Cup winner for that year.

''In hindsight, you could say we could have done it, but we could have been amiss to clubs not saying that the winner of the competition could have been going forward [to the FFA Cup].''