Israel has tonight decided to free hundreds of foreign activists detained aboard a Turkish-backed aid flotilla to Gaza, including some it had threatened to put on trial.

Sources in Israel told Reuters that cabinet ministers had made the decision amid rising world protests against Israel's raid of the flotilla yesterday. The raid resulted in the deaths of at least nine people. Tonight it emerged that some 680 activists seized on the boats would be released.

"It was agreed that the detainees would be deported immediately," Nir Hefez, a spokesman for Israeli Prime Minister Benjamin Netanyahu, said in a written statement

Israel's security cabinet said it regretted the killings in the interception of the Gaza bound flotilla but called the incident an act of defence against violent provocation.

Ministers said in a statement they regretted the loss of life in the raid, but blamed activists who they said assaulted soldiers who boarded the ship for any fatalities.

Israel said it would continue a naval blockade of the Gaza Strip it has imposed as part of a general embargo on the territory's border crossings.

Earlier today, Taoiseach Brian Cowen warned there would be “most serious consequences” should any harm come to Irish citizens involved with an aid flotilla destined for Gaza.

Both Mr Cowen and Minister for Foreign Affairs Micheál Martin called on Israel to allow Irish humanitarian ship, the MV Rachel Corrie, pass through its military blockade of Gaza.

The cargo vessel is ploughing ahead with its attempt to deliver aid to Gaza despite yesterday’s deadly attack by the Israeli navy on a Gaza-bound flotilla.

Mr Cowen called today called for the immediate establishment of "a full, independent international inquiry into yesterday’s events, preferably under UN auspices”.

He called on Israel to release "unconditionally" Irish citizens who he said had been taken to Gaza by the Israeli authorities and asked to sign papers allowing for their deportation.

Speaking in the Dáil during Leaders' Questions, the Taoiseach said said the presence of Irish diplomatic personnel in Israel provided "better prospects" that the citizens would be released "sooner rather than later"

"But I will make this point. If any harm comes to any of our citizens, it will have the most serious consequences.”

Mr Cowen said Ireland’s longstanding position was that the Israeli blockade of Gaza was “immoral and counterproductive” and should be ended.

“Israel must listen and respond to the clear concerns of the international community on this issue. To do otherwise will only serve to reinforce the position of the extremists on both sides and jeopardise the hope of achieving some urgently needed political progress in the region, which the current proximity talks represent," he said.

The Israeli army has warned that it will be stopped if it attempts to enter Israeli waters.

The Rachel Corrie, which has five Irish nationals and five Malaysians aboard, is due to arrive in Gazan waters over the coming days, a spokeswoman for the Irish Palestine Solidarity Campaign said. It became separated from the main aid flotilla after being delayed for 48 hours in Malta due to logistical reasons, and is currently off the coast of Libya.

Mr Martin, who called Israeli Ambassador Dr Zion Evrony to a meeting yesterday, said the boat should be allowed through peacefully.

Mr Martin said Israel was also obliged to respect its international obligations under the Vienna Convention and ensure Irish citizens have access to full consular support. He also expressed his condolences to the Turkish government and the families of the people killed when Israeli commandos raided the Turkish registered Mavi Marmara aid ship in international waters as it travelled from Cyprus, killing nine people.

Five Irish campaigners - including leading activists Dr Fintan Lane and Fiachra Ó Luain - are being held in the Be’er Sheva detention camp, from where they face deportation. Dr Lane and Mr Ó Luain were on board Free Gaza boat Challenger 1 which was boarded by Israeli forces.

Two Irish people, including activist Shane Dillon, have been deported and are expected at Dublin airport late tonight. The Irish ambassador in Tel Aviv was given permission to meet Mr Dillon at Ben Gurion Airport before his departure. It is understood Mr Dillon said he was treated well. Officials have been waiting to see the other detained Irish citizens during the day.

Nobel laureate Maireád Corrigan-Maguire, former UN assistant secretary general Denis Halliday, film maker Fiona Thompson and husband and wife Derek and Jenny Graham are the Irish nationals on board the Rachel Corrie.

Speaking from the ship today, Mr Graham said the vessel was carrying educational materials, construction materials, medical equipment and some toys. “Everything aboard has been inspected in Ireland,” he said. “We would hope to have safe passage through.”

However, an Israeli marine lieutenant, who was not identified, told Israel's army radio his unit was prepared to block the Rachel Corrie. "We as a unit are studying, and we will carry out professional investigations to reach conclusions," the lieutenant said, referring to yesterday's confrontation. "And we will also be ready for the Rachel Corrie," he added.

Additional reporting: Reuters