Officials from the Department for Exiting the European Union have warned that the government would struggle to implement the systems and infrastructure needed for Boris Johnson’s Brexit deal by the end of the transition period in 2020.

In a paper prepared last week and seen by the Financial Times, DExEU warned that “delivery of the required infrastructure, associated systems, and staffing to implement the requirements of the protocol by December 2020 represents a major strategic, political and operational challenge.”

The protocol refers to the elements of the prime minister’s deal that would govern trade between the Republic of Ireland and Northern Ireland, which would take place without checks under the plan, and from Britain to Northern Ireland, where checks could be required.

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Under Johnson’s exit agreement with European leaders, EU customs rules would apply to Northern Ireland-Republic of Ireland trade. Goods moving directly from Great Britain to Northern Ireland would not be subject to a tariff unless they were deemed “at risk” of being moved into the EU afterwards. Likewise, goods from third countries entering Northern Ireland would be subject to the UK tariff, unless they were likely to be moved to the EU.

Customs checks and controls could therefore apply to goods moving from Britain to Northern Ireland, although Johnson has recently denied this, but no checks or controls would be required between Northern Ireland and the Republic.

This dual-tariff regime has replaced the customs union in the original backstop, but the DExEU leak said that “delivery on the ground would need to commence before we know the outcome of negotiations” on the future relationship between the UK and the EU.

Both sides have said they would try to complete these negotiations within the transition period lasting up to the end of December 2020, but this has been deemed unlikely, with former head of the UK’s permanent representative to the European Union Sir Ivan Rogers warning this represents the biggest challenge of Brexit. “I am not saying – never have said – that no trade deal of any sort is possible next year. I am saying, as I was well over three years ago, that a serious, wide coverage, FTA cannot and will not get done in that time,” Rogers said last month.

The Delivering the Protocol by December 2020 document, which was marked “Official Sensitive”, discussed the possibility that the government would not be ready to put in place new systems and procedures to cover trade with Northern Ireland by the end of next year, according to the FT.

DExEU told the paper it “did not comment on leaks”.

This is the latest in a number of leaks that have questioned whether Johnson would be able to implement his Brexit plan by the end of 2020 if he is returned as prime minister after Thursday’s election.

On Friday, Labour leader Jeremy Corbyn released a Treasury report suggesting there would need to be customs checks in the Irish Sea under the deal.

The report stated that "customs declarations and documentary and physical checks [West-East] and [East-West] will be highly disruptive to the NI economy”. There have been conflicting signals form government as to whether such checks would be necessary, with Brexit secretary Steven Barclay stating that they would, after official advice, and Johnson saying they would not.

Corbyn said the Treasury document, which said there were "potential fetters" in the proposal, provided "cold, hard evidence" that Johnson's plans would create further red tape for goods passing between Northern Ireland and Great Britain.

"What we have here is a confidential report by Johnson's new government, marked 'official sensitive', that exposes the falsehoods that Boris Johnson has been putting forward," he said.

"This is cold, hard evidence that categorically shows the impact a damaging Brexit deal would have on large parts of our country."

The Conservatives insisted the plans were an "initial assessment" drawn up by junior civil servants and which had never been seen by Johnson or senior ministers, while Johnson insisted the analysis was "wrong".

Johnson said there would "absolutely not" be new checks, adding: "The deal we've done with the EU is a brilliant deal... unlike the previous arrangements it allows the whole of the UK to come out of the EU including Northern Ireland and the only checks that there would be, would if something was coming from GB via Northern Ireland and was going on to the Republic."

Asked if he believed Barclay was wrong to suggest there would be new checks, he added: "Yes”.

“Because there's no question of there being checks on goods going NI-GB or GB-NI because... we're part of the same customs territory and it's very clear that there should be unfettered access between Northern Ireland and the rest of GB... the whole of the UK comes out of the EU.

"We're a UK government, why would we put checks on goods going from NI to GB or GB to NI? It doesn't make sense."

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