The centre-back has not featured since the start of September, with a second-half substitute appearance in a 4-1 Johnstone's Paint Trophy defeat at Dagenham his only outing this season.
And he will now have to undergo surgery to correct his ankle complaint.
Boss Joe Dunne told Colchester's official website: "Josh needs an ankle operation and that will keep him out for three months.
"He had been making some progress in rehab and had reached a certain point in his recovery but the ankle is still very sore.
"Josh visited the specialist on Wednesday for further investigation of his ankle and it has now been agreed that he should have the operation."
- Sports & Recreation