The 29-year-old has gone under the knife after suffering a knee injury against Boreham Wood last weekend.
It appears the problem is worse than first feared and Justin Edinburgh must do without the former Cheltenham and Oldham player until well into the New Year.
“The club are disappointed to confirm that James Dayton is likely to miss the next few months following a knee injury.
“He underwent surgery this afternoon and will work closely with the club's medical staff in a period of rehabilitation.
“We wish James all the best in his recovery and look forward to seeing him return to action soon.”
Manager Justin Edinburgh backed his team to respond after losing 1-0 to Wood last weekend.
“That is what I will say about this group, in my year in charge every time we have lost we have come up with the right answers,” the manager said.
Orient face Beaconsfield at home in the FA Trophy this weekend.