Last year's Federation Cup winner Belconnen United has been granted an exemption to enter at the quarter-final stage of the ACT FFA Cup qualifying rounds.
Capital Football also admits it's disappointed with Football Federation Australia's decision to restrict each club to entering one team in this year's FFA Cup.
Eighteen teams from Capital Football will contest the second edition of the nationwide knockout tournament, which pits A-League professionals against amateurs and semi-professionals from across the country.
Belconnen United will come in at the quarter-finals after winning last year's Federation Cup, but not playing in the FFA Cup.
Tuggeranong United represented the ACT last year, beating South Hobart before hosting A-League giants Melbourne Victory in front of more than 5000 fans at Viking Park, with the match shown live around the country.
Belconnen United had originally asked Capital Football to bypass the qualifying rounds and face the ACT winner in a playoff, but club president Jaime Garrido was satisfied with the outcome.
"At the end of the day we've got to do what's best for football in the region," Garrido said.
"Last year was an anomaly with Tuggeranong.
"In an ideal world we would be representing the ACT, but it is what it is and we're more than happy coming in at the quarter-finals."
Capital Football clubs will enter the competition in the third round with the aim of securing the one place reserved for an ACT team in the main draw.
Clubs were able to enter several teams from various divisions in previous years of the Federation Cup, but the FFA has decided to limit each club to one team.
Capital Football chief executive Heather Reid said the move was designed to increase the standard of the competition and to remove the confusion of two teams from the same club playing each other.
"The FFA has said that it is one team, one club," Reid said.
"That's been a bit disappointing, but again, this is a FFA competition we're part of and FFA is controlling the eligibility of teams."
Six of the 10 State League teams entered in the FFA Cup - ANU FC, Brindabella Blues, Canberra City, Goulburn Strikers, Lanyon United, Narrabundah, O'Connor Knights, Queanbeyan City, Weston-Molonglo FC and White Eagles - will be drawn to play each other in the third round in April.
The remaining four State League clubs will receive a bye to the last 16.
They will be joined by National Premier League teams Canberra FC, Canberra Olympic, Cooma Tigers, Gungahlin United, Monaro Panthers, Tuggeranong United and Woden-Weston FC.
Meanwhile, Capital Football is awaiting approval from the FFA before it can announce who will be the new coach of W-League champions Canberra United.
An announcement is expected to be made this week.
Championship-winning coach Elisabeth Migchelsen has accepted a position as the assistant coach for the South African women's national team.