Northern Ireland temporarily suspended some inspections at two ports late Monday after threats of violence and increased tensions have been reported in the area.
Graffiti was discovered in Belfast describing port staff as "targets." Staff have also reported suspicious behavior such as people writing down license plate numbers.
Police say they are increasing patrols near ports of entry.
A spokesman for the European Commission announced Tuesday they had withdrawn European Union staff from the Northern Ireland ports as a safety precaution and condemned the violence.
Many pro-British unionists fiercely oppose the new trade barriers introduced between Northern Ireland and the rest of Britain as part of the Northern Ireland protocol, a stand-alone deal for the region after Britain left the EU.
The protocol was designed to maintain the principles of the 1998 Good Friday Agreement and Northern Ireland's open border with Ireland by keeping the region in the British customs territory but also aligned with the EU’s single market for goods.
The British-run region remains deeply divided along sectarian lines, even after the 1998 peace deal, with Catholic nationalists aspiring to unification with Ireland and Protestant unionists wanting to remain part of Britain.