Ships, including one from Ireland, were intercepted in international waters and warned not to pass an Israeli sea blockade.
Israeli military claim they came under gunfire and knife attacks first, with at least ten pro-Palestinian activists killed and four soldiers wounded.
In a statement released by the Ireland Palestine Solidarity Campaign, it has been claimed three Irish nationals are known to be unhurt.
The group has said that Shane Dillon is on a plane back to Ireland, while Dr Fintan Lane and Fiachra O Luain have both contested deportation and are now in an Israeli detention camp and will be brought to court within 72 hours.
Speaking through group, Dr. Lane's father Jim said: "I am proud of my son, not only for going on this solidarity mission to Gaza, but also for refusing deportation.
"He is making a point that Israel should have no control over who enter Gaza. He has done nothing wrong and I support him.
"Furthermore, it is my belief that the United States should stop giving carte blanche to the Israeli state, for it is this support that gives Israel the confidence to act with such impunity."
A large crowd gathered outside Belfast City Hall on Monday afternoon to protest against the action taken by Israeli commandos, as other demonstrations took place across the UK and Ireland.
One demonstrator told those assembled - who carried placards and banners and shouted pro-Palestinian slogans: "We have to do something - we cannot keep silent all these years.
"We have been silent. They have silenced us.
"You cannot criticise Israel, they are above the law, they are above everything - NO. They are the criminals."
Sinn Fein President Gerry Adams was among those in attendance.
"I welcome the fact that Michael Martin has sent for the Israeli ambassador and has indeed sent the Irish ambassador to check out the wellbeing of the Irish nationals," he told UTV.
"But thus far, there seems to be a complete close-down, clampdown, on any information coming out of the flotilla."
The action taken by Israeli commandoes has been condemned by both the British and Irish Foreign Ministers.
"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," said Michael Martin.
William Hague said the British embassy was in "urgent contact" with the Israeli government, asking for more information.
He said: "I deplore the loss of life during the interception of the Gaza flotilla. Our embassy is in urgent contact with the Israeli government.
"We are asking for more information and urgent access to any UK nationals involved.
"We have consistently advised against attempting to access Gaza in this way because of the risks involved. But at the same time, there is a clear need for Israel to act with restraint and in line with international obligations."
Among others on board the Irish ship, the MV Rachel Corrie, was Nobel peace prize winner Mairead Maguire.
In 2009 she was arrested and detained in Israel after attempting to defy the blockade by sailing a boat load of aid into Gaza.
According to Amnesty International, Ms Maguire is believed to be safe.
"The family have lost contact with Mairead, but believe her to be safe, as this boat (the MV Rachel Corrie) was delayed leaving Cyprus and is behind the boats which were intercepted," said Northern Ireland Amnesty spokesman, Patrick Corrigan.
Amnesty is now calling for Israeli authorities to conduct an immediate, independent, investigation and to make public the rules of engagement issued to the troops involved.
"Israeli forces clearly appear to have used excessive force," Mr Corrigan continued.
"Israel says its soldiers acted in self-defence, alleging that protestors attacked them, but it seems incredible that the level of lethal force used by Israeli troops could have possibly been justified."
Footage has emerged showing pandemonium on board the Mavi Marmara, with activists in orange lifejackets running around as others tried to help a colleague lying on the deck.
Co Tyrone man John Hurson, who represents the pro-Palestinian group Viva Palestina, was due to have been onboard the lead vessel.
"No one on board was armed - they were all humanitarians taking aid to Gaza," he told UTV.
Sinn Fein councillor on Derry City Council, Gerry MacLochlainn, was deputy leader of a previous aid convoy to Gaza and is appalled by the apparent attack in international waters.
"It is time now for the International Community to act and Ireland should lead this action," he said.
"Israel must be brought to book and made amenable to international law like everyone else."
Holocaust survivor Hedy Epstein, 85, and a number of Euro MPs were also on board the ships caught up in the strike.
Sinn Fein MEP Bairbre de Brún has spoken out against Israel's actions.
"The EU must suspend its preferential trade agreement with Israel and ensure that it can only be re-instated if Israel ends its blatant disregard for international law and basic human rights," she said.
A spokesman for the Israeli embassy in London has said: "We have no doubt regarding the real intention of the flotilla. It's not about humanitarian aid.
"You can see clearly from the footage that when they boarded they were attacked with knives and sharp metal objects and left with not much option but to respond."
Pictures of activists with sticks bludgeoning an Israeli soldier as he tried to land on a boat from a helicopter were shown by Turkish channel NTV.
Satellite news channel al-Jazeera reported from the lead Turkish ship saying Israeli forces fired and boarded, leaving its captain wounded.