The First Minister has said a deal between the UK and EU would be in "everyone's best interests".
There are just weeks left until the end of the Brexit transition period.
The Northern Ireland Protocol, part of the Brexit divorce deal, will see the region continue to enforce the EU's customs rules and follow its rules on product standards.
Arlene Foster said the EU Future Relations team in the Executive Office is co-ordinating readiness planning across all departments, including an option for a non-negotiated outcome.
She said the group was initially meeting on a monthly basis but is now meeting on a fortnightly basis.
"This work builds on preparations made in the lead up to a potential no-deal exit in 2019," she said.
"And while we are preparing for a non-negotiated outcome, it is important to remember that the protocol will still apply in that scenario.
"Whilst the non-negotiated outcome is very different from a no-deal Brexit, which Operation Yellowhammer was dealing with this time last year, there are similar themes and issues arising.
"A lot of preparatory work for Yellowhammer was undertaken and we're building upon that in the event of a non-negotiated outcome, and I very much hope that isn't the case."
SDLP MLA Pat Catney put concerns to Mrs Foster that even in the event of a deal being agreed, preparations are "too far behind in implementing parts of the Northern Ireland Protocol to avoid major disruption at the end of the transition period?"
Mrs Foster said: "Of course the best outcome would be for an agreement between the European Union and the United Kingdom so that we can move forward together."
But she said there is an acknowledgement that some issues around the movement of goods will not be ready in time.
"That's the same whether goods are coming from the Republic of Ireland through Northern Ireland into Great Britain, or indeed from other places in the European Union into Great Britain, so there have already been some ways of dealing with the pressure that is undoubtedly there," she said.
"I welcome the fact that there is that acknowledgement because it gives some certainty to our companies.
"We'll continue to work with our colleagues in the UK Government to try and get more clarity for our businesses because we do recognise there is very much a need to provide clarity for our businesses and our citizens as well."