Eight Irish people were travelling on a flotilla of aid ships where a reported 15 people have been killed in clashes with Israeli commandos.
ichael Martin, Foreign Affairs Minister, said consular officials are working to confirm the safety of Irish people caught up in the incident.
"I am gravely concerned at the reports emerging of the storming of a Turkish ship by Israeli commandos," the minister said. "My department is seeking to establish the full facts of what has occurred and confirm the safety of the eight Irish nationals who sailed with the Turkish-led flotilla.
"The reports of up to 15 people killed and 50 injured, if confirmed, would constitute a totally unacceptable response by the Israeli military to what was a humanitarian mission attempting to deliver much needed supplies to the people of Gaza."
The flotilla, which had been warned it would not be allowed to pass an Israeli sea blockade, was carrying about 10,000 tonnes of aid and 800 passengers on eight ships.
It is understood the Turkish Mavi Marmara ship, from the pro-Islamic aid group IHH, and Free Gaza's Challenger 1 were intercepted by Israeli Navy ships in international waters, 80 miles off the coast of Gaza.
Three Irish people, Dr Fintan Lane, Fiachra O Luain and Shane Dillon were on board the Challenger 1 which had travelled from Cyprus in the first wave of the flotilla.
The Ireland Palestine Solidarity Campaign (IPSC) said it has not been able to contact any of its members on the ships.
Dr David Landy, IPSC chairman, accused Israel of breaching international law. "The fact that Israel would allow its forces to kill and wound international human rights activists shows the world once again that Israeli is a rogue state that acts with impunity," he claimed.
The Irish owned vessel, the Rachel Corrie, is part of the convoy.