Brussels' chief Brexit negotiator has made the case for Northern Ireland remaining in the European Union customs union after Britain leaves the EU, to solve a deadlock in talks over the Irish border.

Michel Barnier said there were already over 100 areas where Northern Ireland implemented special rules to harmonise with the Republic and argued that Brexit called for a "specific solution" to "unique circumstances".

Speaking at a think-tank in Brussels the senior EU official said "those who wanted Brexit" must come up with solutions to solve the conundrums it had created.

"We need to preserve stability and dialogue on the island of Ireland. We need to avoid a hard border. I know that this point is politically sensitive in the UK, it is not less sensitive in Ireland," he told an audience at the Centre for European Reform.

"Some in the UK say that specific rules in Northern Ireland would endanger the integrity of the UK single market. But Northern Ireland already has specific rules, in many areas that are different to the rest of the UK.

"Think of the all-Ireland electricity markets… think of rules that prevent and hinder animal disease. There are over 100 areas of cross-border cooperation on the island of Ireland and such cooperation depends in many cases on the application of common rule and common regulatory space."

Failure to introduce new customs system in time for Brexit would be ‘catastrophic’

Theresa May has committed to taking the UK out of the single market and customs union, but the decision means new difficulties on the Irish border.

Ireland will be staying in the EU, Britain will be leaving, but neither side wants to tear up the Good Friday agreement and put a hard border on the island of Ireland.

Irish PM Leo Varadkar has expressed concern over the Brexit border arrangements (AFP/Getty Images) (AFP/Getty)

The EU however says that its must still have a border on its frontiers, and has suggested in leaked internal documents that customs checks instead be carried out at ports between Northern Ireland and Great Britain.

Brexit Secretary David Davis has however ruled out a “new border in the UK”, arguing that such a solution would risk “the constitutional and economic integrity of the United Kingdom”.

The Conservatives also have no majority in the House of Commons and would likely rely on votes of the Northern Ireland unionists DUP to pass any Brexit deal, limiting the Government’s freedom of action on the subject.

In a wide-ranging speech, Mr Barnier called for clarity from the UK over the issue of the Irish border.

"The UK said it would continue to apply some EU rules on its territory, but not all rules," he told the audience. "What is therefore unclear is what rules will apply in Northern Ireland after Brexit and what the UK is willing to commit to avoid a hard border. I expect the UK as a good guarantor of the Good Friday agreement to come forward with proposals.

Brexit: the deciders Show all 8 1 /8 Brexit: the deciders Brexit: the deciders European Union's chief Brexit negotiator, Michel Barnier Getty Brexit: the deciders French President Emmanuel Macron Getty Brexit: the deciders German Chancellor Angela Merkel Reuters Brexit: the deciders Commission President Jean-Claude Juncker EPA Brexit: the deciders The European Parliament's chief Brexit negotiator Guy Verhofstadt Getty Brexit: the deciders Britain's Prime Minister Theresa May Getty Images Brexit: the deciders Britain's Chancellor of the Exchequer, Philip Hammond PA Brexit: the deciders After the first and second appointed Brexit secretaries resigned (David Davis and Dominic Raab respectively), Stephen Barclay is currently heading up the position PA

"The Islands of Ireland is faced with many challenges, those who wanted Brexit must come up with solutions."