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.
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.