Team England issued a statement admitting that an “administrative error meant that she was not formally entered into the race”.
For the 21-year-old Lowther, it meant that months of preparation work focused on this specific event had come to nought.
“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 had paid off.
“While Team England have apologised, I’m still gutted not to have an opportunity to represent my country after all the hard miles I’ve put in.”
Team England chef de mission Sarah Winckless said: “I personally shared my apologies for missing her out of the time trial today.”
She said her team had failed to put the proper information into the Games’ Sports Entry System, despite ‘seven or eight’ opportunities to catch the error.
“No athlete should be put in this position because of an administrative error by my group.”
England appealed to the Commonwealth Games Federation but that was rejected.
“It’s disappointing that at the ‘Friendly Games’ the Commonwealth Games Federation couldn’t step in and do something about it,” said British Cycling performance director Stephen Park.
“Her training programme has been focused on this and she missed a number of races in the run-in so she has been really peaking. In that regard from an athlete and team perspective it’s really disappointing because we were really keen and eager to see what performance she could actually put down.”
Park said Lowther was not a contender to win the time trial, but said “to say she was going to be miles off the medals would be unrealistic.”
Lowther will now get one more chance to compete in these Games in Saturday’s road race.
“She’s trying to be as upbeat as she possibly can,” Park added. “She’s really taken it incredibly maturely.
“She’s been out on a training ride this morning and we’re now all behind her efforts for the road race. Hopefully she’ll come out there feeling fresh and be able to get a little bit of retribution on the road.”
Team England must hope this is the only incident of its kind here. Winckless said extra checks had been carried out but stopped short of a 100 per cent guarantee.
“I would give you 99.9 per cent sure,” she said. “I thought we were in a really strong position that we had done the job we were meant to do for the whole team. It became clear yesterday that’s not the case.”
The former world champion rower clearly sounded upset as she faced the media.
“It’s hugely emotional,” she said. “As an ex-athlete I know exactly how hard Melissa has worked. Her focus has been on this event and this is not what I wanted for any of our Team England athletes.”