Health officials have said their "primary concern" is seeking assurances that medical and health care supplies will not be interrupted after the Brexit transition period.
Around 98 per cent of medicines used in Northern Ireland are transported from Great Britain through local ports.
The majority of those are distributed through the UK wholesaler network.
Cathy Harrison, head of the EU exit transition unit in the Department of Health, said that Northern Ireland will remain aligned with the EU on medicines and medical devices, however Great Britain will not.
The Department of Health unit, which consists of seven staff, oversees the department's readiness for Brexit.
Outlining some of the key issues to Health Committee, Ms Harrison said there are concerns around the requirement for goods moving from Great Britain to Northern Ireland to abide by importation rules.
"There may be a number of mitigations we may need to introduce to avoid the risk of any delay that may occur in our medicine supplies coming as a result of additional check or tariffs", Ms Harrison added.
She also told the committee that there will be at least 11 statutory instruments coming through the committee in relation to EU transition.
The civil servant also told the committee that there is ongoing work to look at issues around east-west implications for both the supply and regulation of medicines in Northern Ireland.
The committee was told that Northern Ireland will have to comply with particular EU directives, including the Falsified Medicines Directive (FMD), however Great Britain will not.
"Our continued compliance with FMD raises a number of issues relating to medicine supplies and regulation and a 12-month derogation has been requested via the UK government to the EU to allow time for various mitigations to be put in place," she added.
Turning to the controversial Internal Market Bill, Ms Harrison said the unit has sought legal advice on the implications of their ongoing work.
"Since July there has been an acceleration of activity in relation to both national contingencies and work relating to the Northern Ireland protocol," she added.
The committee deputy chair Pam Cameron asked whether any of their concerns has been alleviated by the Internal Market Bill.
Ms Harrison said their initial view on the proposed Bill is that it relates more to west-east issues.
"My primary concern during the next few months is assurances around our medical and health care supplies and no interruption to those when we end transition period," she explained.
SDLP MLA Colin McGrath raised issues about staffing levels in healthcare.
He said it is "commonly accepted" that a "sizeable amount" of the health workforce is from outside of the UK.
He added: "There could be a worst-case scenario where there are hundreds of staff that go home and that don't come here to make this their home and we are left with the deficit of staffing."
He also raised issues around the impact of a no-deal scenario on current levels of stock.
He queried how long it would take to replenish the levels.
Ms Harrison told the committee there is a "multi-layered approached", adding that health authorities have a lot more stock in the UK than it normally would.
