Foreign Affairs Minister Micheal Martin has repeated calls for Israel to allow aid boat the MV Rachel Corrie through its military blockade of Gaza.
As activists held during a commando assault which left nine dead prepared to leave the region, Mr Martin said it was imperative the Irish-owned ship and its humanitarian cargo were let through.
"I again repeat my urgent call to the Israeli government to allow safe passage of the Irish-owned vessel, the MV Rachel Corrie, which is still sailing towards Gaza to deliver its consignment of humanitarian aid," the minister said.
"It is imperative that there should be no further confrontation or bloodshed arising from what has been all along a purely humanitarian mission by those involved in the Gaza flotilla.
"The Government will be maintaining close contact with the Israeli government on this issue in the coming days."
Mr Martin welcomed Israel's decision to release all 679 people taken off the flotilla of aid ships during the military assault on Monday.
Among them are six Irish activists, including Fintan Lane and Fiachra O Luain, Australian journalist Paul McGeough, two Irish-Libyan passport holders and a naturalised Pole.
"I am pleased that, in response to the clear calls made by many in the international community, including the Irish Government and the UN Security Council, Israel has now decided to release immediately all those still in detention after being seized in international waters on Monday morning following the storming of the Gaza convoy," Mr Martin said. "I look forward to the prompt and safe return of the six Irish citizens who still remain in Israeli custody."
The crew of the MV Rachel Corrie, which includes Nobel peace prize winner Mairead Maguire, former United Nations diplomat Denis Halliday and three other Irish people, expect to hit the exclusion zone around Gaza on Friday or Saturday.
It is understood five Irish citizens have been taken by bus from the Be'er Sheva detention camp in southern Israel on a two-hour drive to Ben Gurion Airport in Tel Aviv. They are expected to be put on flights out of the country. Isam Bin Ali, a naturalised Irish citizen who was born in Libya, has reportedly already left Israel for Ireland.