Last week Downing Street hit back at European Commission President Ursula von der Leyen after she displayed a “disappointing” lack of understanding of the anger in some communities in the Six Counties.
The EU chief reiterated her offer to find “practical solutions” to the issues arising from the protocol – but stood firm on the need for checks to be carried out on goods entering from Britain.
Loyalists argue that the introduction of a border in the Irish Sea effectively cuts off Northern Ireland from the rest of the UK.
Ms Dudley Edwards warned of the growing threat of violence from pro-Union communities in the Six Counties.
She said the post-Brexit arrangement “has convinced the extremes of loyalism that only the threat of violence will get rid of it”.
She added: “At present they’re confining themselves to street protests.”
Ms von der Leyen last week said the protocol remains the “only possible solution to ensure peace and stability in Northern Ireland while protecting the integrity of the European Union’s single market.”
The spokesperson said it was the responsibility of both the UK and the UK to find a “pragmatic” solution to the problems which have appeared in the Six Counties since the start of the year.
They added: “The protocol relies on the support of all communities in Northern Ireland so it is disappointing that there was not more recognition from the Commission president of the impact that the current operation of the protocol is having in Northern Ireland.
“While the EU prioritise protection of the single market and treat the regulatory boundary as if it were like any other external EU border, our focus remains on protecting the Belfast (Good Friday) Agreement in all its dimensions”.
The protocol is a key part of the Withdrawal Agreement signed by Boris Johnson and EU bosses.
The arrangement means Northern Ireland effectively remained in the EU’s single market for goods after the Brexit transition period expired last December 31.
Unionists have expressed anger over checks being carried out on imported goods at ports in Belfast and Larne.
They fear the changes will lead to a distancing between Northern Ireland and the rest of the UK which could pave the way for the reunification of Ireland.
On Saturday hundreds of protesters took to the streets of Portadown in County Armagh to call for the protocol to be scrapped.
One speaker who addressed the crowds accused the Prime Minister of “betraying the Union”.