Healthcare arrangements will be plunged into chaos if the UK triggers a hard Brexit.
Among the worst hit will be patients in the Republic who want to avail of an EU scheme that allows them to have the treatment paid for in Northern Ireland or the UK mainland, Department of Health officials warned.
Question marks also hang over other existing healthcare arrangements, such as the European card which allows Irish tourists in the UK or the North free care for minor injuries.
Other areas that may have to change include care for patients from the Republic who need treatment in the UK for an illness or condition that is not treatable here.
The potential obstacles were outlined by officials from the Department of Health at the Oireacthas Health Committee yesterday.
However, several members of the committee accused the Department of being too complacent about the threat of Brexit to Irish patients and called for a more proactive approach.
Under the cross-border health directive, patients from the Republic can travel to another EU state for treatment and be reimbursed for the cost. Last year 1,700 of these treatments were paid for and around 700 travelled to Northern Ireland.
It is the cheapest location for travel and the most convenient in terms of distance.
Officials said it was likely other Irish patients had been treated in other hospitals in the UK, but the HSE had yet to provide the figures despite being asked weeks ago.
It was known that of 613 patients from the Republic who availed of the scheme, at least 574 were treated in the UK.
The officials said arrangements whereby cancer patients from the Republic are treated in Derry should be protected by agreement.