The Emirates Arena was to host the event from 9-12 April but the EJU changed its mind in a sponsorship row.
It objected to the partnership British Judo had with Ultimate Fighting Championships to promote the event.
The championships will now be held in Baku, Azerbaijan as part of the inaugural multi-sport European Games.
British Judo chairman Kerrith Brown said: "British Judo believes that throughout its partnership with the EJU, it has consistently acted in a professional and diligent manner, based on what we feel is in the best interests of the sport and the athletes competing at the European Championships.
"It is with great reluctance and disappointment that I have to confirm the cancellation, following the EJU's decision to withdraw the hosting rights."
Scotland enjoyed enormous success in judo during last year's Commonwealth Games, landing 11 medals, with team flag bearer Euan Burton and the Renicks sisters, Kimberley and Louise, among six gold medal winners.
Earlier this month, the Renicks sisters spoke to BBC Scotland about how important home backing would be in April as they seek vital Olympic qualification points.
In a statement published on its website, the EJU said: "The European Judo Union has come to the realisation that the British Judo Association does not fit the EJU criteria to host the EJU flagship event.
"The BJA had entered into a sponsorship agreement which did not meet the EJU values. BJA persisted in this, notwithstanding that it had been warned on a number of occasions that this arrangement was unacceptable to the EJU, which has a right under the event contract to approve or disapprove any sponsorships of EJU events."
British Judo has accepted "with great reluctance" the decision by the European Judo Union (EJU) to strip Glasgow of the European Championships.