The European Union and United Kingdom are to hold talks with the North's First and Deputy First Ministers today to discuss how to manage security concerns which halted some checks at Belfast and Larne ports.
Arlene Foster and Michelle O'Neill and the European Commission vice-president Maros Sefcovic and British cabinet minister Michael Gove will meet via video conference to discuss the North's post-Brexit arrangements.
The commission is also in touch with UK authorities “from a security perspective”, a spokesman said.
On Monday night staff carrying out post-Brexit checks at Larne and Belfast ports were withdrawn from duty due to an “upsurge in sinister and menacing behaviour” and threatening graffiti referring to them as “targets”.
The commission told its officials not to attend work yesterday, saying its first priority was their safety.
The PSNI later played down the threat, saying there was “absolutely no information” loyalist paramilitaries were involved and that their assessment was that “individuals or small groups” were responsible.
Ms Foster is also expected to discuss the protocol with British prime minister Boris Johnson, who called last night for "urgent action" from the EU to resolve outstanding problems with the implementation of the protocol.
The DUP yesterday evening warned North-South relationships could not continue as normal and it would stop all cross-border activity related to the protocol as part of a plan to have Northern Ireland "freed from the protocol".
Unionist parties oppose the protocol because it places a border in the Irish Sea between Northern Ireland and Great Britain.
Sinn Féin leader Mary Lou McDonald accused the DUP of recklessness and urged it to “pull back”, saying the majority in the North opposed Brexit and the protocol protected the Belfast Agreement and the economy.
Tensions have been heightened in the North following a blunder by the European Commission on Friday in which it cited the sensitive article 16 provision of the protocol in an initial version of a regulation before hastily reversing course.
The commission said according to its information, the security situation at the ports had “arisen some time ago” and the threats had originated before the article 16 controversy.
"Whatever the reason of threat of violence it's simply unacceptable, full stop. You don't look for excuses, that must be very, very clear, " commission spokesman Eric Mamer said.
The threats have also been condemned across the political spectrum North and South, and in Great Britain.