Cabinet Office Minister Michael Gove has warned that the chaos in moving goods between GB and Northern Ireland "will get worse before it gets better".
r Gove said he was in discussions with the NI Executive, working to ensure "that businesses in Northern Ireland can continue to have access to the rest of the UK market, and that Northern Ireland businesses can have the goods that they need on the shelves, that they have access to at the moment".
On Friday night DUP minister Edwin Poots called on the UK Government to take immediate action to prevent the Northern Ireland Protocol causing further damage to the local economy - but faced criticism from political rivals.
Mr Poots warned there could be food shortages if changes were not made.
There has been an escalation in reports of bare supermarket shelves, freight delays, and disruption to parcel services and commercial traffic.
"I have met senior members of Her Majesty's Government to highlight the scale of the problem, and urged them to take steps up to and including invoking Article 16 as it is evident that the Protocol is damaging Northern Ireland at the economic and societal level," Mr Poots tweeted.
"I met hauliers, supermarkets, and processors this week.
"Jobs will be lost in processing, costs of transportation will rise, a wide range of frozen/chilled foods will be unavailable after the temporary exemption period ends."
The DAERA Minister - whose own Stormont Department is responsible for the implementation of EU customs checkpoints at NI ports -blamed the increasing commercial difficulties on political opponents.
"The issues at our ports are a result of the Ireland Northern Ireland Protocol supported by SF, SDLP and Alliance Party," he tweeted.
Responding SDLP leader Colum Eastwood said: "You broke it, you own it."
Alliance MP Stephen Farry also hit back: "Most people well know how DUP helped to deliver a destructive Brexit and the resultant need for special measures for NI. For now, our focus is on mitigating and managing the fallout of DUP's actions," the North Down MP tweeted.
Sinn Fein MLA Martina Anderson also tweeted: "Own it Edwin you and other Brexiteers caused this unmitigated disaster. If you didn't know this was going to happen because of Brexit, you were asleep at the wheel."
Marks & Spencer has already had to suspend nearly 400 of its food product lines in NI due to EU bureaucracy imposed under the NI Protocol since Jan 1.
Chief executive Steve Rowe explained how their Percy Pig sweets are a typical example. "Percy Pig is actually manufactured in Germany, and if it comes to the UK and we then send it to Ireland, in theory, he would have some tax on it. So we've got a lot to do in terms of composition and rerouting, but it's really important that we continue to be focused on trading the business."
Meanwhile, DUP MP Ian Paisley called on Mr Gove to invoke Article 16 of the Northern Ireland Protocol, which permits the UK to act unilaterally if the Protocol causes "serious economic, societal or environmental difficulties... or to diversion of trade.". However experts have said triggering Article 16 would not be an automatic quick fix.
Meanwhile, the Ulster Unionist Party on Friday tabled a recall petition in the Assembly to address the disruption to trade caused by the Protocol.