Ireland’s freight transport industry has warned of “huge disruption” to important supply chains once pre-Brexit stockpiles are run down in coming weeks, saying the country’s economically-significant agricultural and pharmaceutical sectors risk long delivery delays because of new red tape.

Freight bosses have called on Micheál Martin’s government to seek EU exemptions from onerous customs, sanitary and phytosanitary paperwork for several months so they can adjust to the new regime.

The industry was “struggling to keep the flow of goods moving” because of issues with the tax authority’s new pre-boarding notification system, new safety and security declarations and import/export declarations, said the Freight Transport Association of Ireland, a trade group.

But Leo Varadkar, the deputy prime minister, insisted there was “no fix” to the new requirements because of Britain’s withdrawal from the EU single market and customs union.

“There’s no workaround. There’s no set of easements or light-touch regulations that get around that. This is something that transport companies, retailers, wholesale operators all need to embrace the reality of,” he told reporters in Dublin.

The association said supply chains had suffered a “significant shock” since the end of the UK Brexit transition on December 31. The association includes Kerry and Glanbia, two of the country’s food groups, and BWG and Musgrave, big retail wholesalers.

In a letter to Mr Martin, the FTAI said the UK was “out of bounds” for almost all exporters who traditionally send shipments to the European mainland via Britain because of potential Brexit delays, but there was not enough capacity on direct freight routes to the continent. “Hauliers with bookings on direct services are being bounced because of overbooking,” it added.

The letter warned of a “growing backlog of goods of all hues”, saying car parts, electrical household goods, furniture, clothing and food supplies were sitting in depots because there were not enough agents to process the declarations correctly.

“In addition, there are issues with the systems and there are problems with providing enough support and guidance on the new requirements to industry to make this work. The net result will be that companies operating on very tight margins will cease trading, creating unemployment, supply lines will disappear, and the consumer will be left with less supply and increased prices.”

The FTAI called for an “adjustment period” of up to six months to facilitate a shift to the new regime, saying new requirements “could not be tested by industry” before it went live on December 31. A transition period should be used to train customs agents and inspectors and test IT systems, the association said.

The Irish government said it “fully recognises” the challenges to business after Brexit. While the move from frictionless trade was always going to cause disruption, many business were “working effectively” with the tax authority to adopt the new regulations.

Mr Varadkar acknowledged there were “a lot of teething problems”, saying the authorities were helping “as best we can”. But he added: “It doesn’t change that basic fact that the fundamental rules of trade between Britain and Europe . . . have now changed. So it either means adapting to the new rules or finding alternative supply chains.”