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The announcement comes as no surprise as Parkinson tendered his resignation to the newly-promoted club only for it to be refused.
The U's manager has been strongly linked with the vacancies at Sunderland and Hull City in recent times as well as Premiership Charlton.
Peter Heard, chairman of Colchester United, has decided to hold Parkinson to his contract until it expires in a year's time.
"The directors, management and fans of Colchester United Football Club continue to hold manager Phil Parkinson in the highest regard," read a statement on the club's official website.
"The decision to seek an injunction to prevent him tearing up his contract is in part in a vain hope that he will change his mind.
"However, in truth, it is more about the principle of ensuring that the process of a football club losing an excellent manager, albeit for all the right reasons, is conducted in the appropriate manner, adhering to the contractual legal considerations and taking into account the significant financial implications to the club of losing its star manager to a key competitor at a time when it has just gained promotion.
"Colchester is taking this bold move because it fundamentally believes that even the football world has to take employment contracts seriously.
"This injunction is about making a stand, but it is also a very clear signal to Phil Parkinson and any club making him an approach, that Colchester United puts a very high value on the manager that led the club to success this year - a very high value indeed.
"Phil Parkinson is contracted to stay with Colchester United until May 31, 2007."