The European Commission expects permanent post-Brexit border control posts to be ready in Northern Ireland by the middle of this year.
Commission spokesman Daniel Ferrie said the UK had obligations to meet under the Northern Ireland Protocol, which governs the trade in goods from the rest of the UK.
Irish Sea checks required under the terms of the protocol are currently taking place at existing repurposed port buildings and other temporary facilities.
A Stormont powersharing minister representing the DUP has been challenged by devolved executive colleagues over his controversial decision to halt work on permanent inspection posts.
Mr Ferrie said: “We have received reassurances that these announcements last week are not going to affect the current work of the temporary border control posts in Northern Ireland, so the relevant checks and controls are continuing to take place as usual.
“We expect the same commitment when it comes to the UK Government’s obligations under the protocol regarding the permanent facilities that need to be put in place by the middle of this year, by the middle of 2021, in line with the protocol and also in line with the Joint Committee decisions from last December.”
Permanent facilities are due to be built at Belfast, Larne, Warrenpoint and Foyle ports.
Physical construction has not commenced at any of the sites, with work currently still in the design and preparatory phases.
The DUP and other unionist parties in Northern Ireland are pushing for the protocol to be ditched, claiming it has driven an economic wedge between the region and Great Britain which undermines the union.
The move by DUP Agriculture Minister Gordon Lyons to abandon the building projects at the ports was debated during a scheduled meeting of the Stormont executive on Monday.
Ministers from Sinn Fein, the SDLP and Alliance Party, the three pro-remain executive parties, contend that he does not have the authority to act unilaterally on issues considered significant or controversial.
Rival Stormont Assembly members on Monday accused Mr Lyons of stunt politics.
He replied: “The steps that I have taken are as a result of the practical barriers and the legal uncertainties that currently exist.
“I think the steps that I’ve taken have been entirely reasonable and I would ask people whether their opposition to what I have done is based on common sense and practicality or is it just based on opposition to anything that they don’t like in relation to Brexit and the protocol.”
It is understood Attorney General Brenda King has advised that, under the terms of the ministerial code, Mr Lyons would be required to bring such proposals to the wider executive.
Mr Lyons is set to hold talks with Ms King ahead of further discussions on the matter on Tuesday.
Explaining his rationale on Friday, Mr Lyons said his move was in response to the “practical difficulties” caused by the protocol.
He cited uncertainty over the movement of goods when grace periods currently limiting protocol bureaucracy end at the start of April.
The minister has said he did not expect the permanent border posts to be ready until the middle of next year.
He told the PA news agency on Friday: “The latest information I have on it is that the final builds wouldn’t have been in place until the end of the 2021/22 financial year. So that would have been really this time next year.”
That was timetable before his move to halt work on Friday.