The meeting between the UK's Michael Gove and the EU's Maros Sefcovic on the Withdrawal Agreement comes after Britain unveiled plans to break international law over it.
Brussels reiterated on Monday that it will "not be shy" in using legal means to ensure the Brexit Withdrawal Agreement is respected.
"The Withdrawal Agreement is to be implemented, not to be renegotiated — let alone unilaterally changed, disregarded or disapplied," European Commission's Maros Sefcovic told reporters following a meeting with Britain's Cabinet Office Minister Michael Gove.
"It cannot be stressed enough that the (Ireland/Northern Ireland) Protocol is specifically designed to protect the Good Friday (Belfast) Agreement and the achievements of the peace process, including avoiding a hard border on the island of Ireland," he added.
Sefcovic also reiterated that Brussels has given London until the end of the month to withdraw the contentious parts of its draft Internal Market bill and that it is "considering all legal options available" and will "not be shy" in using them if London fails to do so.
However, Britain's Cabinet office said in a statement released after the meeting that "the measures set out in the United Kingdom Internal Market Bill are designed to create a 'safety net' to ensure the communities of Northern Ireland are protected."
"The UK is clear that those measures would not be withdrawn," it added.
UK and EU positions 'far apart'
Tensions between the two sides were ratcheted up earlier this month when British Prime Minister Boris Johnson unveiled the draft legislation which would allow his government to override parts of the Withdrawal Agreement.
The Brexit treaty, which was renegotiated by Johnson and approved by parliamentarians earlier this year, sets the terms of the country's exit from the EU. It plans for Northern Ireland to remain part of the bloc's customs union in order to avoid a hard border seen as key to safeguarding peace on the Irish island.
Johnson argues the bill will protect the Good Friday Agreement and will ensure that goods continue to flow uninterrupted between Northern Ireland and Great Britain but the country's opposition, the European Commission and Washington have all condemned the bill.
Sefcovic also warned on Monday that "the window of opportunity" to put in place the operational measures needed to ensure the Ireland/Northern Ireland Protocol functions properly "is rapidly closing".
The transition period will expire at the end of the year.
"I have therefore reiterated the urgent need to the UK to accelerate its work on all aspects of the Protocol and in particular with regard to sanitary and phytosanitary controls; customs-related IT systems; and the registration of Northern Irish traders for Value Added Tax purposes".
"Many difficult issues remain and the UK's positions are far apart from what the EU can accept," he went on.
For its part, Britain said it "reiterated the importance of commitment by both sides to upholding obligations under the Withdrawal Agreement and protecting the Belfast (Good Friday) Agreement in all respects".
Fewer than 100 days
Sefcovic and Gove's meeting — their third one — also addressed other urgent matters including citizen's rights.
The EU official said he raised "serious concern over the UK settlement scheme" and how it "distinguishes between different categories of EU citizens with the same resident status".
"We cannot have two classes of beneficiaries of the Withdrawal Agreement," he said.
According to him, the scheme would see some EU nationals in the UK deprived of benefits including income support, housing allowance or health insurance which he described as "unacceptable" for the bloc.
The UK said it "underlined the need for timely and proper implementation of citizens' rights commitments by the EU and member states".
"The UK reiterated its commitment to supporting EU nationals in the UK, as well as UK citizens in the EU, whilst remaining clear that measures undertaken by the UK must supplement and support the work done by the EU."
Sefcovic also highlighted that there are now "fewer than a hundred days" before the transition period ends and that "much work remains to be done" to ensure "a full, timely and effective implementation" of the Withdrawal Agreement.
The warning comes just a day ahead of the next round of talks to hammer out a post-Brexit trade deal between the UK and the rest of the bloc.
A deadline of mid-October has been set to reach an agreement, with the transition period set to end on December 31.
Talks have been deadlocked for months with the issues of Northern Ireland, fishing rights, and open and fair competition proving to be particularly contentious.
Failure to reach an agreement will mean reverting to World Trade Organisation rules which would cause long delays in the flow of goods and services between the UK and the continent.