Within hours of the polling booths opening, the hashtag #deniedmyvote was trending on Twitter.
Administrative errors, a lack of correct forms being sent out to voters and late registration were blamed for the inability of people to cast their ballot.
Agata Patnya, an immigration and human rights barrister, tweeted: “Turned away from polling station this morning. Told I should vote in my EU member state.
“I registered before the deadline. Have been here since 2005. Voted many times before. This is my member state.”
Marcella Finazzi wrote on Twitter: “Just went to vote this morning with my orange poll card and I was told I cannot vote because I figure as Italian citizen not British Italian.”
Another user showed photos of her registration with a London borough council but claimed she was still turned away.
“As an EU citizen I was denied my right to vote in the hostile UK,” she wrote on Twitter.
Lewisham Council were among the boroughs helping voters this morning after they found themselves unexpectedly unable to vote.
They asked people listed as “ineligible to vote” when they turned up to their polling station to call them and they would try and investigate.
EU citizens needed to fill out two forms to vote in the European election in the UK.
The first was a register-to-vote form and the second was a declaration to vote in the UK form which needed to be returned to local authorities by May 7.
The Electoral Commission advised councils to tell their EU citizens about the second form but did not have a legal duty to do so. There appears to have been a difference in how local councils have informed EU citizens about this two stage process.
Lisette Slegers Tweeted: “Was turned away at the polling station in Thanet this morning. Am on the electoral roll but never received the form.”
Felicidad Martinez Tweeted: “My name was on the list at the polling station but crossed with a G next to it, which apparently means I can’t vote. Did the form but never received polling card.”
However some think that EU citizens needed to be better prepared.
Twitter user @Arwenstar, who is French and living in the UK, wrote: “I find this #DeniedMyVote hashtag extraordinary.
“You denied yourself your vote by not being prepared. How funny that this is happening to EU nationals who are of course diehard Remainers—you live in this country, enquire about the procedure over here.”
The Electoral Commission said it was aware of some EU citizens living in the UK being unable to vote.
It said the “very short notice” from the Government about the UK taking part in the election had hampered efforts to raise awareness of the process for EU citizens transferring their vote from their home country.
A spokesman said: “If an EU citizen instead chooses to vote in the EU election in the UK, there is a process for them to complete to essentially transfer their right to vote, from their home member state to the UK.
“This is a requirement of EU law, which specifies that this has to be done ‘sufficiently in advance of polling day’. UK law sets this as 12 working days in advance of the poll.”
The Electoral Commission spokesman said the legal process “could be made easier for citizens, and the Commission made the case for doing so following the last EU elections in 2014”.
They added: “However, improvements to the process are reliant on changes to electoral law, which can only be taken forward by Government and Parliament.
“The very short notice from the Government of the UK’s participation in these elections impacted on the time available for awareness of this process amongst citizens, and for citizens to complete the process.
“EU citizens’ right to vote in the election in their home member state remains unaffected by the change in the UK’s participation; in order to do so, they would need to be registered in that country in accordance with that country’s process and timetable.”