A Ukip MEP has quit his post as a party whip after a controversial anti-Islam campaigner was cleared to stand in the party’s leadership election.

Mike Hookem said he was resigning as deputy whip in the European Parliament after the chief whip, Stuart Agnew, declared his support for Anne Marie Waters.

Waters, founder of the Sharia Watch pressure group who previously called Islam “evil”, is one of 11 candidates cleared to run in the leadership contest by the Ukip national executive committee.

Previously, the party’s leaders had blocked her from being a candidate in June’s national election, citing her views on Islam.

Former leader Nigel Farage says Ukip will be “finished” if it becomes an anti-Islam party.

Hookem said he was not prepared to “turn a blind eye” to extremism: “I strongly disagree with the views Ms Waters and Mr Agnew promote and I would like to put as much distance between me and them as possible.

“If I were to continue in my position of deputy whip, I would be seen as supporting or at the very least turning a blind eye to extreme views and this is not something I am prepared to do.”

“I am not a racist and have never campaigned on race issues. While I do believe in controlled immigration, this position is about space rather than race; and I am not prepared to support someone who seeks to single out a section of our society simply due to their religious beliefs.”

However, Peter Whittle, the Ukip deputy leader – seen as the favourite to become leader – strongly defended Waters’s right to run.

“The whole thing was done very rigorously. There was a vetting process. We all had to go through it and if you all get through that then you absolutely have the right to stand. That means Anne Marie should be able to stand,” he told BBC Radio 4’s Today programme.

Whittle also spoke out against the growing number of Sharia courts, which are used to settle disputes in some Muslim communities in accordance with traditional Islamic law, saying there could only be one legal system if the country was to unite effectively.

“Ukip has always been a party that does talk about issues that other people do not like to talk about,” he said.

“There are at least 80 courts that we know about. The problem is that the people who suffer the most in these courts tend to be women because they are often about domestic issues and often women who go before the courts don’t actually know their rights as a British woman.

“There has got to be one legal system. Certain things happen in Sharia courts which do go against the spirit of our laws.”

Whittle denied that his comments were anti-Islamic. While acknowledging that the rulings of such courts were not legally binding, he said there was great pressure on participants to accept their findings.

“The government itself is having an inquiry into Sharia law. This is something that is obviously of great importance. If you have a single legal system then you can have a more united country,” he said.

“You cannot have a situation where there are increasing courts where people can choose. You can’t have separate communities with their own legal systems.”

The contest was triggered by Paul Nuttall’s decision to stand down following the collapse of the Ukip vote in June’s general election.

Whittle rejected the idea that there was no longer a role for Ukip following the Brexit vote to leave the European Union.

“What people are seeing more and more is a political establishment which in one way or another is chipping away at the idea of Brexit. We have got to be the guard dogs of that,” he said.