The freight industry has warned of the potential for a fresh Brexit ferry fiasco after it emerged all British truckers will be required to have counter-terrorism safety security certificates to enter the European Union in the event of no deal.

The EU rule was introduced after the 9/11 attack on New York’s twin towers but only applies to third country freight entering the EU.

But if the UK crashes out of the bloc it will be classified as a third country like Ukraine or China and all freight operators will be required to fill out a 38-point safety and security form.

Irish drivers using the UK as a land bridge to the continent would also have to comply, sources said.

Not only would this be necessary for every consignment, but it would be required hours before transit, fuelling fears that trucks could face delays not just because of customs and public health checks but also safety.

James Hookham, the deputy chief executive of the Freight Transport Association, said it was a serious issue particularly because the certificates were required for each consignment in a truck, affecting small- to medium-sized businesses which have multiple pickups before they head to the continent.

“It is not fiscal like customs and tariffs, but it is more serious for ferries and Eurotunnel because it involves security issues because the vessel or train could be endangered if there is a truck without the security certificate on it,” he said.

The concerns have been raised amid reports that truckers could face fines of up to £1,000 if they do not have a similar clearance certificate on their way back into the UK.

And to add to the freight industry’s problems, the Department for Transport (DfT) only has 9% of the 11,000 driver permits requested by British hauliers to operate legally in the EU in the event of no deal.

The government confirmed the need for safety and security clearance certificates in a 37-page “partnership pack” it has prepared for importers and exporters.

“For imports into the UK a separate safety and security declaration needs to be made by the carrier of the goods (this is usually the haulier, airline, freight train operator or shipping line, depending on the mode of transport used to import goods),” the pack says.

Hookham said the safety certificates were not as big an issue for ports such as Felixstowe that deal with sea containers, because goods from countries such as China have weeks of transit in which to deal with paperwork.

But the just-in-time systems used in British manufacturing rely heavily on the “turn-up-and-go” arrangement that operates at ports and Eurotunnel.

Under the EU rules ferry companies would need paperwork two hours in advance while Eurotunnel would need it one hour before transit.

An HM Revenue and Customs spokesperson said: “HMRC have written several times to traders to advise them how to prepare for a no deal and will continue to set out further detail over the coming weeks.”

The concern over safety certificates comes amid mounting worries among the freight industry of a no-deal Brexit.

In the event of no deal all heavy goods vehicle operators would be required to have a European Conference of Ministers of Transport (ECMT) permit, of which only 984 have been allocated to the UK for 2019 and just 60 for Northern Ireland.

Last week the DfT confirmed it had received 11,000 applications for permits from 2,000 truck operators.

Seamus Leheny, the policy manager for the FTA in Northern Ireland, tweeted that he received a call on Tuesday from a haulier who operates to and from the continent who had applied for 35 ECMT permits but had been “told they get 2”. Leheny said: “You don’t need to explain the consequences of this.”

Pauline Bastidon from the FTA tweeted that she had been told of another company that “applied for 60 permits and got just 14”.