He had the backing of the Professional Footballers Australia group and they will likely appeal the decision, while the Phoenix have also vowed to not give up on signing McGlinchey.
"The Wellington Phoenix, as an interested party, will seek legal advice on this decision as it raises questions as to whether or not McGlinchey and other players have been, and are actually contracted to, the legal entity that holds the license for the Central Coast Mariners to play in the A-league," the Phoenix said in a statement.
The PFA also released a statement this evening, which outlined their stance on the matter.
"The PFA stands by the advice given to Michael, which was based on information given in October 2013 by Football Federation Australia (FFA) that due to a change in ownership, the A-League licence of the Mariners would be transferred to a new company controlled by owner Mike Charlesworth.
"Under an agreement reached between FFA and the PFA, all Mariners players were to be offered employment with the new company, and the previous Mariners entity would cease to operate the A-League licence. As a result, almost the entire Mariners squad has signed agreements with the new entity.
"As Michael was contracted to the previous entity, he was free to pursue his professional interests as an uncontracted player and sign a contract with a club of his choice.
"However, it only recently emerged that the entity licensed to operate the Mariners had not changed, but will do so in the near future. The reason for the failure to transfer the licence has not been satisfactorily explained to the PFA.
"The PFA is greatly concerned by the situation at the Mariners, which unnecessarily raises concerns about the sanctity of the A-League licensing system administered by FFA. All A-League players are entitled to know that the club which employs them is duly licensed by FFA. If not, the ability of the game to regulate itself and uphold player contracts is brought into question."
The Phoenix are due to open the A-League season against Perth in Wellington on October 12.