The Taoiseach has been in contact with EU Commission President Ursula von Der Leyen to raise concerns about the decision to override part of the Northern Ireland Brexit protocol in order to block vaccines entering the North.
There are concerns in Government that this risks undermining the agreement.
A spokesperson for Micheál Martin told RTÉ News that the Taoiseach was aware of the issue and is "in discussions with Ursula Von der Leyen to raise concerns about this."
DUP Leader and First Minister of Northern Ireland Arlene Foster earlier described the triggering of Article 16 as "an incredible act of hostility".
She said the EU is prepared to use Northern Ireland "when it suits their interests".
"At the first opportunity the EU has placed a hard border between Northern Ireland and the Republic of Ireland over the supply chain of the coronavirus vaccine," she said.
The leader of the SDLP said invoking article 16 is "disproportionate and a grave error in judgment by the European Commission.
"We face a common threat. Our response should be characterised by our common values - cooperation and solidarity. We're engaging with both governments and the EU to find a way forward," Colum Eastwood said.