The Irish border could yet snag Boris Johnson’s Brexit deal, with experts saying it will be impossible to deliver the computer systems for the special arrangements for Northern Ireland by the end of this year. Failure to implement the new systems will risk legal action by the European commission against Britain, the Institute for Government says.

In a new report, it says: “The [Brexit] deal has the support of no Northern Irish political parties and it looks almost impossible to complete the practical changes, for government and business, by the end of the year. Failure to comply with the withdrawal agreement could see the European commission begin infringement proceedings and the UK ending up at the ECJ [European court of justice].”

Brexit deal: EU may threaten 'to block' City's access to its markets Read more

Johnson’s government remains adamant that there will be no checks or new reporting systems on trade crossing the Irish sea, despite Ireland and the EU insisting that those would have to be in place to protect the Irish border.

The prime minister’s intention to establish a trade deal with the EU by the end of December 2020 was also dealt a blow by Simon Coveney, Ireland’s deputy prime minister, at the weekend as he indicated the bloc would be in no rush to work to Johnson’s timetable.

In a blunt assessment of the likelihood of satisfying Johnson’s “ambitious” vision, he said the fact that Britain had put the timescale for a trade deal into law did not mean the other 27 European countries would fall in line. “In my view, it’s probably going to take longer than a year,” he said.

The IfG’s report says HMRC has previously stated similar systems to the proposed customs arrangements for Northern Ireland would take five years to develop and implement.

Part of the problem is that until the new trade deal between the UK and the EU is struck, the details of the Northern Ireland arrangements cannot be finalised.

The complicated system for Northern Ireland involves the region effectively staying in the single market but in the UK customs zone. This potentially means tariff charges and rebates, paperwork and physical checks on certain fresh foods and live animals going from Great Britain to Northern Ireland.

In the new report, “Getting Brexit done: what happens now?”, the IfG says Brexit will be far from done on 31 January when the UK formally leaves the EU with the expected ratification of the withdrawal agreement ending the article 50 process.

“The UK will formally leave the EU at the end of January, and in that sense Brexit will be done, but many of the biggest Brexit jobs will be far from over,” it says. “It will continue to dominate government for years to come. The prime minister may hope to end Brexit’s dominance in the public debate after 31 January, but in Whitehall it will continue to be the biggest and most challenging task faced by a government in decades.”

Under the deal sealed by Johnson with the EU last October, animals and fresh food going from Great Britain to Northern Ireland will be subject to some physical checks, with a tariff and tariff rebate system operating for the first time. These are there to protect any substandard goods seeping into the EU’s single market through smuggling over the Irish border into the Republic of Ireland.

While all sides recognise the complexities of the new system, little public attention has been paid to the fact that new computer systems cannot be designed by either HMRC, ferry companies, or manufacturers or suppliers like Tesco until the trade deal with the EU is done.

The report says: “With the details of how the border will operate still unclear – and likely to be so for some months – and no preparatory work having happened for checks between Great Britain and Northern Ireland, the 11-month timeline is almost certainly undeliverable.”

It notes that Sir Jon Thompson, a former chief executive of HMRC, said that a similar customs systems involving rebates could take up to five years to develop and implement.

Coveney issued his warning on BBC One’s Andrew Marr Show, saying the deal to be struck between the UK and EU over their future relationship was vast, encompassing security, data, aviation and trade.

He said: “When people talk about the future relationship in the UK in particular, they seem to only talk about a future trade agreement. Actually, there’s much more to this than that … I know that Johnson has set a very ambitious timetable to get this done – he’s even put it into British law – but just because a British parliament decides that British law says something, doesn’t mean that that law applies to the other 27 countries of the European Union.

“And so the European Union will approach this on the basis of getting the best deal possible, a fair and balanced deal, to ensure that the UK and the EU can interact as friends in the future. But the EU will not be rushed on this just because Britain passes a law.”