The 22-year-old, who won two gold medals at the UCI World Championships last year, had recently taken time out of cycling due to an enforced medical rest.
And in the race to get fit and take her place in Wales' squad, James sustained an injury to her knee ruling her out of contention for Glasgow.
"I'm terribly disappointed I won't be competing in Glasgow," said James, who won a silver and bronze at the 2010 Commonwealth Games in Delhi.
"I still hope to be there cheering the team on, and I wish the entire team the best of luck.
"In May, I received abnormal results from a routine smear test and, following the biopsy results, I underwent minor surgery which I'm pleased to say was successful.
"The surgery, however, meant [taking] two weeks away from my usual training regime.
"Following the rest, in an effort to make up for lost time, I aggravated a knee injury that will rule me out of the Games."
- Sports & Recreation