“This is not easily reconciled with the government’s assertion that Northern Ireland remains within the UK customs territory,” said Professor Alan Winters, of the UK Trade Policy Observatory, at the University of Sussex.
Furthermore, the new analysis warns that Mr Johnson’s agreement – under which the UK will leave the EU by the end of January, if he wins the general election 2019 – will break the law.
It contravenes the Taxation (Cross-border Trade) Act 2018 which prohibits “arrangements under which Northern Ireland forms part of a separate customs territory to Great Britain”.
The Northern Ireland “protocol” has become a growing controversy in the campaign, after the prime minister abandoned his previous promise never to agree to a customs barrier with Great Britain.
On Sunday, Mr Johnson claimed there would be no checks on goods flowing between Northern Ireland and Britain – despite his withdrawal agreement stating there will be – saying that wouldn’t “make sense”.
But the analysis by the trade observatory has found that about 82 per cent of Northern Ireland’s imports from non-EU countries would face new tariffs from Brussels.
They would also be charged on approximately 64 per cent of imports from Great Britain – and therefore on around three-quarters of all Northern Irish imports.
The study also echoes fears already raised by the Democratic Unionist Party that British companies will increasingly shun Northern Ireland over time, because of the new barriers.
It warns that mainland exporters are likely to “lose market share” in Northern Ireland because of the imposition of tariffs.
In addition, it suggests it will be “difficult” to introduce the promised system of rebates for buyers of UK goods in Northern Ireland, if they are not destined for the Republic.
Professor Winters added: “A free trade agreement between the UK and the EU would not completely avoid the problem.
“While goods produced in Great Britain exported to Northern Ireland and transiting on to the Republic of Ireland would face no tariffs, they would still need to satisfy rules of origin to prove that they had been produced in Great Britain.
“Hence there would still be administrative hurdles for such exports to jump.”