The failure was blamed on a combination of administrative errors, a lack of correct forms being sent out to voters and late registration.
The fact that the UK’s involvement in the elections was confirmed late because of the Brexit crisis was also said to have been a key factor.
EU citizens were required to fill in a form called the UC1 or EC6 to declare they would be voting in the UK and not their country of birth, but councils are said to have failed to communicate with EU citizens about the forms.
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It is also claimed that councils did not send out the forms to people who requested them on time and also failed to register the forms when they were received.
Between one and two million EU citizens living in the UK were unable to vote after what has been branded a "scandal” caused by the registration process, according to a civil rights group.
The UK Electoral Commission said it would be reviewing the treatment of EU citizens in the election but UK Socialist MEP Claude Moraes said more should have been done to stop it happening in the first place.
His colleague Seb Dance said he was “dismayed” at people being denied their vote.
"It is absolutely heartbreaking that despite our best efforts, EU citizens have been denied the vote and on such a massive scale” Roger Casale, New Europeans
Moraes, chair of the Justice Committee in the last Parliament, wrote to UK Home Secretary, Sajid Javid about the “depressing” and “extraordinary disenfranchisement” of voters on an important election for EU citizens.
New Europeans, a group campaigning for citizens’ rights, said the situation was a “scandal we knew was coming.”
In a letter dated 25 April to UK Deputy Prime Minister David Lidington MP, the group called for the additional administrative measures required of EU citizens to be completed at polling stations.
Despite cross-party support in Parliament for the measures it put forward it says these calls fell on "deaf ears."
Its founder Roger Casale said at the time: "Neither the government nor the Electoral Commission can hide behind the lame excuse that the elections were confirmed late in the day.”
“Both organisations should have made contingency plans given that the Government did not have a stable majority and could not be relied on to deliver Brexit on 31 March.”
“Those plans should have included putting timely and adequate measures in place for EU citizens to be able to vote in the UK elections. They have failed to do so," he added.
New Europeans surveyed electoral registration officers and, based on the evidence collected so far, says that only between one in three and in some instances one in five EU citizens were able to return their UC1 forms in time.
"It is absolutely heartbreaking that despite our best efforts, EU citizens have been denied the vote and on such a massive scale.”
“EU citizens did not have the vote in the [Brexit] referendum and have missed out again now through no fault of their own. This utter chaos will certainly have a material impact on the election and may call the legitimacy of the results into question.”
“The UK government may even have a case to answer in court,” Casale added.
Labour MP David Lammy said the election system amounted to “ugly discrimination” for people who had endured “three years of being insulted, exploited and asked to apply to stay in their own homes.”