MEP Jim Nicholson has called for the establishment of a Northern Ireland Brexit advisory council to fill the void created by the absence of an Executive.
British and European negotiators are meeting this week to continue Article 50 talks on the UK's departure from the EU.
The issue of how to deal with the border in Ireland is to be discussed on Wednesday.
UUP MEP Nicholson said that given the lack of a Executive Northern Ireland was under-prepared for Brexit despite it having the "most to lose".
He said: "“Of all parts of the United Kingdom, Northern Ireland has the most to lose from Brexit if a workable deal is not agreed between the EU and the UK. We are after all the only part of the UK to share a land border with the European Union. However, with the lack of a functioning Executive we are also the least prepared.
“In the absence of an Executive I have therefore called on Secretary of State James Brokenshire to establish an advisory council on Brexit, with the main party leaders and the three MEPs from Northern Ireland. I have also urged Mr Brokenshire to come to Brussels to speak with European counterparts about the paper recently published by the UK Government on the Northern Ireland/Republic of Ireland border.
“With negotiations needing to be wrapped up by October of next year, I fear that time is not on our side. We need all parties to get down to business and work together for a Brexit deal that works for Northern Ireland and the entire United Kingdom."
Talks aimed at restoring an Executive are set to resume this week, with more intensive dialogue between the parties to open next week.
Labour has made a dramatic shift in policy on Brexit, announcing it would keep Britain in the EU’s single market and customs union – and accept continued freedom of movement – during a transition period after March 2019.
The European Union has warned the UK it won't allow Northern Ireland to be used as a "bargaining chip" in the Brexit negotiations, saying proposals so far from London on the border were "magical thinking".