Prime Minister Boris Johnson has described disruption to supplies crossing the new Irish Sea border as “teething problems”.
But he said the government will have “no hesitation” in invoking a mechanism which would override the current arrangements if the problems are deemed “disproportionate”.
The DUP and Ulster Unionists have called for the protocol to be revoked.
But Mr Johnson said goods were flowing to NI in “in normal volumes”.
The Irish Sea border is a consequence of Brexit and means that most commercial goods entering NI from GB require a customs declaration.
On Tuesday, the UK’s major supermarkets wrote to the government, warning an “urgent intervention” is needed to prevent further disruption to NI food supplies.
Speaking in the Commons on Wednesday, DUP Westminster leader Sir Jeffrey Donaldson said the government needed to step up.
He quoted a number of examples to MPs about issues being faced by his constituents since the new system of checks had begun on 1 January.
Five of these were:
He also called for the government to extend the three-month grace period for food businesses, which was agreed to allow firms more time to phase in new checks.
The “grace period” means that supermarkets currently do not need to comply with all the EU’s usual certification requirements.
Cabinet Office Minister Michael Gove said talks were ongoing to ensure there was a “sustainable approach” by the end of March, regarding the grace period.
While the prime minister said “so far no lorries have been turned back” and that goods had been flowing “effectively” from GB to Northern Ireland.
“What I can confirm to him is if that if there are problems we believe are disproportionate then we will have no hestitation in invoking Article 16,” he added.
Article 16 of the Northern Ireland Protocol, agreed in the original withdrawal agreement, is essentially a safeguard that would allow the UK or EU to act unilaterally if measures imposed as a result of the protocol are deemed to be causing “serious economic, societal or environmental difficulties”.
The government has so far resisted calls from unionist parties to immediately invoke Article 16, and has said ongoing issues will continue to be worked out through the UK-EU joint committee.
The first goods crossed the new trade border between Northern Ireland and the rest of the UK on 1 January.
Sinn Féin said it has concerns, but met with wholesalers on Wednesday morning.
On Tuesday, it said 95% of the supply of fresh food arriving into Northern Ireland had been restored.