The Deputy First Minister Martin McGuinness described the Israeli intervention as a "raid" and said it was a "completely unacceptable and unjustified use of force".
"The Rachel Corrie should have been allowed to proceed to Gaza without Israeli aggression," he said.
"This is an attack on an Irish flagged vessel and it demands a strong response by the Irish government."
Mary Hughes, one of the founders of the Free Gaza movement, which has been organising aid shipments, condemned Israel's actions.
She added: "We are totally outraged that they have once again gone into international waters and violently boarded the boat, and force people to go to Israel when all we wanted was to be left to get to Gaza."