Welsh welterweight Evans, 23, a silver medal-winner at the London 2012 Olympic Games, did not travel to Glasgow with the Wales team.
No explanation for his refused accreditation was given.
In a statement, the Wales chef de mission Brian Davies said: "Team Wales can confirm that boxer Fred Evans has had his accreditation refused by Glasgow 2014 based on checks completed by the Home Office and the Commonwealth Games accreditation decision board.
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"We have engaged in rigorous and thorough communications with all relevant bodies over the last few weeks, including putting forward two mitigation plans, unfortunately all of which have been unsuccessful.
"The key Welsh and British sporting agencies have been supportive in our attempts to get Fred to the Games and we are bitterly disappointed at the outcome.
"Fred is a world class boxer and has handled this difficult situation in a very disciplined manner, continuing to work hard in the hope of satisfactory resolution."
Evans, a favourite to win gold in Glasgow, was ordered to pay more than 1,000 pounds ($1,700) in fines and costs after admitting his part in an assault in a Birmingham night club in April.
It was unclear if that incident had any affect on the decision to reject his accreditation.
The men's welterweight boxing competition begins on Friday. ($1 = 0.5862 British Pounds)
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