Cathedral chiefs said the presence of Carl Benjamin may be a risk to public order after he became the subject of protests.
Far-right activist Mr Benjamin, who is standing as an MEP in the South West England region, had three milkshakes thrown at him in three days while out campaigning last week.
And on police advice, the University of the West of England cancelled its own hustings where he was due to appear.
Exeter Cathedral authorities invited Ukip to send another candidate instead.
They have invited a range of candidates for the region to speak at Wednesday’s event.
But Ukip’s Tiverton and Honiton branch chairman Margaret Dennis branded the decision to bar the party’s candidate “outrageous” and “an affront to democracy”.
She said Mr Benjamin was an “articulate and intelligent advocate” for the party and for free speech.
Exeter Labour MP Ben Bradshaw told LBC he supported the cathedral's ban, adding Mr Benjamin had “unsavoury views” with “unsavoury followers” and said some “unsavoury things”.
Police are investigating Mr Benjamin for comments about raping Labour MP Jess Phillips.
In 2016 he tweeted to Ms Phillips: “I wouldn’t even rape you, @jessphillips”. He later defended what he called “a joke” and refused to apologise.
In a statement, Exeter Cathedral said: “Under the rules of the Electoral Commission, we may exclude candidates from a non-selective hustings for a number of reasons, including concerns about public order.
“In this case, the cathedral believes that the presence of one particular candidate may cause a risk to public order, given a number of incidents over the last few weeks.
“Ukip has been invited to send another candidate from its list of six candidates standing for election in the South West region.”
One social media user objected to the cathedral decision, posting: “It is obviously not ‘he’ who poses the threat!”
Another accused the authorities of "hating freedom of speech and interfering in our election by de-platforming candidates”.
Anti-far-right campaigners have quickly adopted the tactic of throwing milkshakes during the European elections in attempts to humiliate those they disagree with.
A McDonald’s outlet near to where former Ukip leader Nigel Farage was speaking in Edinburgh was stopped by police on Friday from selling milkshakes because of fears protesters would throw the drinks over him.
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