A border checkpoint is operating again more than a decade after the last permanent border post from the conflict was closed.
Limavady Borough Council has introduced routine checks on cars and passengers at the Magilligan terminal of the Foyle Ferry which links counties Derry and Donegal.
The checkpoints have infuriated passengers and are to be raised with the British and Irish governments by a Fianna Fail senator.
A council spokeswoman said Magilligan was considered “an international port of entry to Northern Ireland and the wider UK”.
Since starting six years ago, the Foyle Ferry has run up to 50 services daily along the mile-long crossing between Greencastle and Magilligan Point.
The car ferry, which has been used by almost two million passengers, has cut journey times between north Inishowen in County Donegal and Limavady in East County Derry from a 40-mile road trip to just 12 minutes.
But the checkpoint has sparked a furious reaction from politicians on both sides of the border.
Fianna Fail senator Cecilia Keaveney said it is doing nothing to “foster good relations” or for the economy.
Limavady Sinn Féin councillor Patrick Butcher said the border checkpoint was “an unnecessary barrier to tourism” and a “burden on rate-payers”.
The issue was raised in the Dublin parliament by Inishowen Fianna Fail senator Cecilia Keaveney in an adjournment debate late on Tuesday night.
In a written reply the foreign affairs minister Micheal Martin said that against the background of what he termed “security normalisation” it was understandable that the checkpoint had given rise to “disquiet”.
“The matter of increased security has been raised by officials in the Department of Foreign Affairs with Limavady Borough Council, which is the relevant implementing body in that jurisdiction, and through the British-Irish Secretariat in Belfast,” he said.
“Limavady Borough Council has advised that these additional checks are due to staff training, which has taken place over the last three weeks. As such it is anticipated that the checks will shortly return to normal levels with only spot checks being carried out.”
Mr Martin welcomed the fact that the issue would be raised at a meeting of the Limavady borough council in the next week. He said his department would monitor the situation.