The UK’s largest supermarkets have warned the government of “significant disruption to food supplies” to Northern Ireland because of “unworkable” post-Brexit border arrangements.

Many supermarkets in the region have been hit by rows of empty shelves because of the new border regime.

But in a letter to Cabinet Office secretary Michael Gove, chief executives of companies including Sainsbury, Marks and Spencer and Tesco UK warned that shortages would worsen when a Brexit grace period, which has exempted retailers from some arduous red tape, ends on March 31.

The supermarkets urged the government to take “a number of steps to work with us to ensure the long-term sustainability of the Northern Irish grocery market”.

The retailers also called on the government to begin an “open discussion” with the EU to explain why implementing the Irish protocol was “unworkable” in the current timeframe, raising the prospect of difficult negotiations with Brussels just weeks after the deal was agreed.

The protocol, agreed by the UK and EU to avoid a hard border on the island of Ireland, means that the region remains under the EU’s internal market controls. New paperwork is now needed to ship from Great Britain, especially for products of animal origin.

The border arrangements, alongside new bureaucracy and the need for certification “in such a short timescale are unworkable”, the supermarket chains wrote in the letter, which has been seen by the Financial Times. The six companies account for most retail food sales in Northern Ireland.

Retailers said the end of the grace period would create more problems for shipping produce to the region. This was because export health certificates signed by a vet would then be needed for all products derived from animals such as meat, poultry, milk and eggs.

The letter said it was “essential we find a long-term solution, agreed with the EU”, before the end of the grace period. “We cannot stress enough that we need time to find and implement that solution.”

The letter was signed by Simon Roberts, chief executive of Sainsbury’s, and Steve Rowe, chief executive of M&S. Tesco UK head Jason Tarry; Roger Burnley, chief executive of Asda; Richard Walker, managing director of Iceland Foods; Jo Whitfield, head of food at the Co-operative Group; and Helen Dickinson, chief executive of the British Retail Consortium also signed.

The retailers said the government needed to tell EU counterparts that changes to the border after April would not be possible — and devise new plans to help ensure the flow of produce and goods.

In the letter, retailers called for a dedicated Cabinet Office group to co-ordinate the government response and create a system integrating customs and food controls. They offered their teams to help develop solutions to address the challenges of operating a just-in-time supply chain.

A government spokesman said: “A new dedicated team in government has already been set up and will be working with supermarkets, the food industry and the Northern Ireland executive to develop ways to streamline the movement of goods.

The spokesman said this was being done in accordance with the Irish protocol, adding: “The grace period for supermarkets and their suppliers is working well, goods continue to flow effectively between Great Britain and Northern Ireland and we are working intensively with industry as new requirements come in.”

Lobby groups in the region have pointed out that discretionary incomes in Northern Ireland are already well below those of elsewhere in the UK, and that any lasting increase in food prices could have a serious societal impact.

Supermarket heads have resorted to unconventional measures to alleviate the difficulties. M&S has dropped several hundred product lines from stores in the region, while Sainsbury’s is selling some Spar products sourced from Ireland to avoid gaps on shelves.

The issue of additional bureaucracy is separate to the problem of tariffs on products dispatched from the UK to stores in Ireland. Mr Rowe last week cited the example of M&S’s Percy Pig sweets, which are made in Germany but exported to Ireland via a UK distribution centre. Because they fall foul of the rules of origin set out in the EU-UK trade deal, they are subject to additional tariffs.

The arrangements under the protocol do not cover companies shipping food products to wholesalers or the restaurant and service trade, leading to haulage groups warning that clients outside the retail scheme are finding the arrangements doubly unworkable.

Peter Summerton, managing director of McCulla Ireland, a major Irish haulier, said those shipping products outside the retail schemes were struggling with supplies.

“If Northern Ireland was not currently in lockdown due to Covid, the restaurant and hospitality industry would be facing severe problems in obtaining supplies from GB,” he said. “There are clear deficiencies in the model and the Road Haulage Association has been warning [the UK environment and food ministry] Defra of these problems since last autumn.”