The 21-year-old had targeted the Gold Coast road time trial as a key point in her season and was selected in February to make the Games.
However, Team England's officials failed to register for event and she did not appear on the start list when it was released on Monday evening in Australia.
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Rather than watch the race on Currumbin beach front, the reigning U23 British road race champion chose to go out on a long training ride to gather her thoughts ahead of Saturday's road race, for which she has been entered.
"I can't put into words how disappointed I am to have been missed off the start list due to an admin error," she said.
"It was one of my targets this season to make selection for the time trial event and I was so proud that my hard work in training has paid off.
While Team England have apologised, I'm still gutted not to have the opportunity to represent my country after all the hard miles I've put in.
"Hearing the news was really difficult and I'd like to thank my family, friends and British Cycling for their support.
"My plan now is to try and put this out of my mind while I focus on preparing for the road race."
And Team England's Chef de Mission, former Olympic rower Sarah Winckless, apologised to Lowther for the mistake.
"I have spoken to Melissa to offer my sincere apologies to her, her coaches and to British Cycling," she said.
"Melissa has trained hard for and focussed on this race and it should never be the case that an error on our part prevents an athlete showing what she can do.
"We appealed to the Commonwealth Games Federation to allow Melissa into the race but it was not possible at such short notice.
"Team England will be conducting a review to understand how the situation has arisen and how it can be prevented from happening again."
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