Fowler was one of seven players whose contracts were terminated when the club was restructured in March after it suffered financial difficulty. He has since joined Perth Glory.
The Professional Footballers Australia (PFA) said they had sought a hearing at Australia's National Dispute Resolution Chamber on behalf of Fowler against the Fury and Football Federation Australia (FFA), who have taken over the club.
"The case is of fundamental importance to all A-League players, as it goes to the heart of the security of a player contract in the A-League," PFA chief executive Brendan Schwab said in a statement on the union's website.
The PFA said they had managed to negotiate settlements for six of the seven players, but were unsuccessful in securing a settlement for Fowler.
"This case is not about the compensation, it is about ensuring contract security for all players in the A-League and more specifically for the players who have suffered from the way in which the FFA handled the player contracts," Fowler said.
"If the A-League is seeking to develop into a competitive league on the world stage, then it needs to get the fundamentals correct and contract security for any professional player is a fundamental principle."
