One football executive called the deal "smoke and mirrors" while at least one club owner is furious at the control Football Australia will still have over the leagues.

The new clubs-run Australian Professional Leagues was unveiled as the new authority running both the A- and W-Leagues and the Y-League when the deal was confirmed late on New Year's Eve.

The new body will be in charge of the commercial and marketing side of the game, while Football Australia will remain the governing power overseeing the bigger picture of the sport.

But although the agreement was hailed as a massive game-changer by Western Sydney Wanderers chairman Paul Lederer on behalf of the clubs, others have questioned the small print in the deal.

According to them, the deal still allows the FA to dictate when the seasons will be played - with a move to a full winter season, favoured by FA, now looking likely.

But A-League clubs are believed to be deeply divided on the issue with some concerned it will be commercially disastrous for the league in the face of competition with NRL and AFL for for TV and media exposure and stadium access, and even with fans facing clashes with their own matches in amateur leagues, as well as cold weather keeping crowds away.

However Football Australia, and reportedly around half the A-League clubs, believe the quality of football would be massively improved by playing in more temperate conditions than in the intense heat of summer, while also aligning seasons with other Asian nations and the NPLs around the country.

Some club owners are also concerned the FA is said to be taking a 10 percent share of club revenues from transfers and also the sale of new and existing club licences, while still holding a veto over the number of clubs playing in the leagues.

The FA refused to discuss the financial terms of the new deal, citing commercial confidentiality, but it's understood the governing body will also receive $3m per year from APL TV and sponsorship rights until 2026, topped up by 10 percent of any league profits.

The new APL board will consist of five club representatives, one FA representative and three independents, but FA will still get to approve who chairs the organisation.

FA have also insisted they can call up A-League and W-League players for national team duties at any time without compensating clubs.

With a packed schedule of games ahead as the Matildas, Olyroos and Socceroos try to catch up for lost time in Olympic preparation and World Cup qualifiers, it could see key players missing A-League and W-League games at the clubs' expense.

The FA will still retain full ownership and control of the yet to be renamed FFA Cup and the NPL, and most importantly the National Second Division, which is intended to create a promotion and relegation pathway for clubs to the APL-run top tiers...and potentially spark a new divide between the APL and FA.

It's understood clubs accepted the deal proposed despite its alleged flaws in a bid to end the years of deadlock over the unbundling, and allow work to finally begin on rebuilding the A-League after years of decline.

The Association of Australian Football Clubs - the body representing the NPL clubs looking to be in the new NSD - has said it will make an announcement about the NSD on January 8.