The European Union's chief Brexit negotiator says checks are continuing on goods coming from Great Britain into Northern Ireland.
Maroš Šefčovič was speaking on Thursday following talks with the British Foreign Secretary Liz Truss.
It comes after the region's Agriculture Minister, Edwin Poots, ordered officials in his department to stop carrying out checks on goods at ports.
This also comes as the resignation of Northern Ireland's First Minister has taken affect since midnight.
After only eight months in the role, the DUP's Paul Givan stood down in protest over the Northern Ireland Protocol as a result of Brexit.
Deputy First Minister, Sinn Féin's Michelle O'Neill, is automatically removed from her post as a result.
Mr Šefčovič says Mr Poots direction is "very unhelpful".
"I believe we must stay laser-focused on practical challenges raised by Northern Irish stakeholders - particularly on the area of customs and the movement of sanitary and phytosanitary goods, in which an understanding could immediately and significantly help operators on the ground, while safeguarding the integrity of the EU's Single Market", he said in a statement after the talks with Ms Truss.
"It is in this context that we see the recent instruction by the Northern Irish Minister for Agriculture to cease sanitary and phytosanitary checks between Great Britain and Northern Ireland as being very unhelpful.
"It creates uncertainty and unpredictability for the people and businesses in Northern Ireland.
"These checks are necessary for Northern Ireland to benefit from access to the EU's Single Market for goods."
But he added: "According to our information, officials in Northern Ireland continue to carry out checks on goods coming to Northern Ireland.
"It is essential that this remains the case. The European Commission will closely monitor the developments on the ground."
He said both teams would continue intensive talks, with another meeting between Mr Šefčovič and Ms Truss set for next Friday.
Johnson's top aides quit
Meanwhile British Prime Minister Boris Johnson is under more pressure after losing four senior aides in the space of a single day.
His chief of staff Dan Rosenfield and principal private secretary Martin Reynolds - who sent a 'bring your own booze' e-mail for a Downing Street party during lockdown - are leaving their roles.
Two other key advisers have also resigned: press chief Jack Doyle and policy chief Munira Mirza.
She was unhappy that he had accused the UK Labour leader, Keir Starmer, of failing to prosecute Jimmy Savile while he was director of public prosecutions.
While the British Chancellor Rishi Sunak - seen as a possible successor to Mr Johnson - also piled pressure on following the row over his Jimmy Savile comments.
Speaking at a news conference, Mr Sunak sought to put distance between himself and Mr Johnson.
"With regard to the comments, being honest I wouldn't have said it and I am glad the prime minister clarified what he meant," Mr Sunak said.
Asked if Mr Johnson should apologise for his remarks, he said: "That's for the prime minister to decide."
Mr Johnson had this week promised a shake-up at Downing Street following the publication of senior civil servant Sue Gray's report into the partygate claims.
But it has been speculated that he was forced to bring forward his plans following the surprise departure of Ms Mirza.
Additional reporting: IRN