A body that claims to represent loyalist paramilitary organisations has told Boris Johnson the outlawed groups are withdrawing support for Northern Ireland’s historic peace agreement.

The Loyalist Communities Council (LCC) said the groups were temporarily withdrawing their backing of the Belfast/Good Friday Agreement amid mounting concerns about the contentious Northern Ireland Protocol governing Irish Sea trade post-Brexit.

However, they stressed that unionist opposition to the protocol should remain “peaceful and democratic”.

The 1998 agreement that loyalist paramilitaries endorsed 23 years ago ended decades of violence and established devolved powersharing at Stormont.

UK ministers are facing a backlash from unionists who fear the post-Brexit protocol threatens Northern Ireland’s place in the UK internal market.

The Democratic Unionist party (DUP) and other unionist parties are pushing for the protocol to be ditched, saying it has driven an economic wedge between the region and Great Britain that undermines the union.

The letter sent to Johnson said the paramilitaries’ stance would continue until the protocol was amended to ensure “unfettered access for goods, services, and citizens throughout the United Kingdom”.

It added: “If you or the EU is not prepared to honour the entirety of the agreement then you will be responsible for the permanent destruction of the agreement.”

The development came as the UK government took unilateral action on Wednesday to extend a grace period that has been limiting the paperwork associated with moving agri-food goods from Great Britain into Northern Ireland.

The EU criticised the move, claiming it risked breaching the terms of the protocol.

Goods arriving in Northern Ireland from Great Britain have been subjected to added processes and checks since the Brexit transition period ended on 31 December.

That bureaucracy is set to intensify significantly when the grace period ends. From that point, supermarkets and other retailers will require EU export health certificates for agri-food products from Great Britain.

The letter to the prime minister was written by David Campbell, the chairman of the LCC. He wrote a similar letter to the Irish taoiseach, Micheál Martin.

The LCC represents the Ulster Volunteer Force, Ulster Defence Association and Red Hand Commando, which were responsible for many deaths during 30 years of conflict.

The main loyalist and republican armed groups signed up to principles such as commitment to non-violence during discussions which led to the signing of the Belfast agreement in exchange for early release of prisoners.

The letter said: “We are concerned about the disruption to trade and commerce between Northern Ireland and the rest of the United Kingdom that is occurring, but our core objection is much more fundamental.”

It said that during the Brexit negotiations the government and the EU said it was paramount to protect the Belfast Agreement and its built-in safeguards for the two main communities in Northern Ireland. The letter said the operation of the protocol “repeatedly breaches those objectives”.

Campbell insisted the LCC leadership was determined that opposition to the protocol should be “peaceful and democratic”.

“However, please do not underestimate the strength of feeling on this issue right across the unionist family,” he wrote.

The protocol is designed to prevent the imposition of a hard border on the island of Ireland by keeping Northern Ireland following EU trade rules.

It has caused disruption to some goods travelling from the rest of the UK as suppliers have struggled to overcome extra red tape.

Police have noted growing discontent in unionist communities. The Chief Constable of the Police Service of Northern Ireland (PSNI), Simon Byrne, previously warned of a “febrile” atmosphere and urged people to step back from the brink of violence.

Inspection staff at ports were temporarily withdrawn from duties this year in response to sinister graffiti, but they resumed their work after police insisted there was no credible threat against them.

Last week Stormont’s DUP agriculture minister, Gordon Lyons, stopped preparatory work on building permanent Irish Sea trade checks at the ports.

That move, the legality of which has been disputed by executive colleagues, did not affect ongoing checks, because those were happening at temporary port facilities.