Johnson-Thompson is in the best form of her burgeoning career, setting the leading score in the world this year and a personal high of 6682 points at the high-class Hypo-Meeting in Gtzis, Austria, last month.
It is a total that would have won gold at last year's World Championships and the third-highest score managed by a Briton, behind Jessica Ennis-Hill and Denise Lewis.
In Gtzis, Johnson-Thompson finished 41 points clear of Brianne Theisen-Eaton, the Canadian world silver medallist seen as her main rival in Glasgow, underlining her status as favourite for the first gold of her senior career.
"I'm absolutely devastated that I'm not going to be able to compete in Glasgow," said Johnson-Thompson.
"The Commonwealths was a key target for me this year and I was feeling so good in my preparation up until this week, so this is a real blow.
"All the advice is telling me that I risk long-term damage if I compete in a heptathlon in just over a week's time and I have to take that advice for the sake of my career. I really hope to be able to compete in the long jump at the European Championships next month but it doesn't take away how gutted I am that I won't be at the Commonwealths."
Johnson-Thompson won long-jump silver at the World Indoor Championships in March and set a personal best in the same event in the Diamond League meet at Hampden Park - a test event for these games - only 10 days ago.
Yesterday Louise Hazel, who won heptathlon gold in the 2010 Commonwealths, suggested competing in that event in Glasgow might have been an unnecessary risk.
"I just question whether that was perhaps a little bit much for her ahead of the championships," said Hazel.
With Ennis-Hill out of the sport after the birth of her son last week and Hazel injured after coming out of retirement to try to make Glasgow, it leaves England with Grace Clements, a bronze medallist four years ago, called up to to fly the St George's flag in the heptathlon.
- Independent