Irish foreign minister Michael Martin has called in the Israeli ambassador to Ireland to explain what happened overnight when it is believed up to 19 people were killed when Israeli commandos boarded ships bound for Gaza with humanitarian aid.
Calls from Sinn Fein to expel the Israeli ambassador from Ireland have been made.
Three Irish nationals who were on board one of the boats are reported to be safe.
Meanwhile, an Irish ship, which was due to be part of the flotilla, was not in the area after it was forced to stop over in Malta for repairs.
The 1,200-ton cargo ship Rachel Corrie was fitted in Dundalk and loaded with supplies before it headed for Gaza and the flotilla organized by a Turkish relief agency of the flotilla.
The Free Gaza Movement along with the Turkish humanitarian organization, IHH, the European Campaign to End the Siege of Gaza and the Greek and Swedish Boat to Gaza organizations were set to sail eight boats led by the Rachel Corrie, loaded with building supplies as well as taking 600 passengers and journalist, to run the Gaza blockade.
The Rachel Corrie was abandoned in the town of Dundalk, near the Irish border by its owners after it was discovered they had not paid the crew, all from Lithuania.
Free Gaza activists bought the ship for $100,000. Union official Ken Fleming told the Irish Times the Irish citizens on board the Rachel Corrie, called after an American activist killed by an Israeli bulldozer, are safe.
"They were delayed because of mechanical problems and only left Malta last night,” he said.
“They want to let their families know they are alright. They told me that they still want to proceed to Gaza with the urgently needed humanitarian aid on board,” he added.
Three other Irish people - Dr Fintan Lane, Fiachra O Luain and Shane Dillon were on board the Challenger 1 , which had traveled from Cyprus in the first wave of the flotilla, said Niamh Moloughney of the Free Gaza Ireland campaign.
"The last email we got from the ship was at 4 a.m. this morning, in which they said the navy were boarding and helicopters were above them," she said.
"I'm in shock. I hope Israel gets called up on its behavior. It's outrageous what they've done. There weren’t even any weapons on board the ship,” she claimed.
The Ireland Palestine Solidarity Campaign has called a protest in Dublin this evening.
Minister for Foreign Affairs Micheál Martin said today he has called the Israeli ambassador to Ireland Dr Zion Evrony to a meeting this afternoon. He stated the ambassador "is currently endeavoring to establish the full facts as they emerge.”
In a statement, Martin said he was "gravely concerned" over the storming of the Turkish ship.
"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," he said.
The Committee on Foreign Affairs announced plans to summon Dr Evrony to an emergency meeting later this week.