Israel's Prime Minister Binyamin Netanyahu has expressed his regret that nine people were killed in the IDF action against the Gaza flotilla.
The six ships, which were part of a supposed aid mission to Gaza, have now docked in the port of Ashdod and 32 activists have been arrested.
Israeli had previously offered the ships a safe passage to dock in Ashdod and have their aid transported by land to Gaza.
Nine activists were killed in violent confrontations on the ship and several more injured. Mr Netanyahu said Israeli troops had been "clubbed, beaten and stabbed" when they boarded the ship.
He said: "There was even a report of gunfire and our soldiers had to defend themselves, defend their lives or they would have been killed.
"Regrettably, in this exchange... people died. We regret this loss of life. We regret any of the violence."
Eight Israeli soldiers have been injured, one seriously. The activists are being held in Ashdod as most refused to sign deportation orders. The injured activists are being treated in Israeli hospitals but some have refused treatment.
The storming of the flotilla has been condemned internationally - and some fear the attack will mean the end of the friendship between Israel and Turkey, its closest Muslim ally. Many of the activists on the ship were Turkish. Turkish Prime Minister Recep Tayyip Erdogan accused Israel of state terrorism and violation of international law.
An emergency meeting of the UN Security Council has been called, in order to draft a resolution calling for an immediate inquiry.
British Foreign Secretary William Hague condemned the attack on ship but said the British government had always warned it would be foolish to attempt to enter Gaza in such a manner.
He said in a statement: "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. It will be important to establish the facts about this incident, and especially whether enough was done to prevent deaths and injuries.
"This news underlines the need to lift the restrictions on access to Gaza, in line with UNSCR 1860. The closure is unacceptable and counter-productive. There can be no better response from the international community to this tragedy than to achieve urgently a durable resolution to the Gaza crisis.
"I call on the Government of Israel to open the crossings to allow unfettered access for aid to Gaza, and address the serious concerns about the deterioration in the humanitarian and economic situation and about the effect on a generation of young Palestinians ."
More than 1,000 people are said to have gone to the Israeli embassy in London to protest against the killings, and many other protests have been held worldwide.