All the 679 detainees taken off the ships during the Israeli military-led action which saw nine civilians killed will be deported within 48 hours, but about 50 will be held for questioning, a statement from the Israeli government said.
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Earlier, Foreign Secretary William Hague said 31 British nationals and a further 11 with dual nationality were known to have been detained after the seizure of the vessels as they attempted to breach the Israeli blockade of the territory.
One Briton who was on one of the ships heading towards Gaza arrived back in Britain last night.
IT professional Hasan Nowarah, from Glasgow, described the moment the aid flotilla was stormed by Israeli troops.
He told Sky News the Mavi Marmara ship was surrounded by helicopters and a Zodiac assault craft. He said the attack happened “out of the blue”.
“All I could hear was screaming and bullets all over the place, over the Marmara, the Turkish ship.
“All you could see was screaming and bullets. Out of the blue as I looked around our ship, all I could see were hundreds of Zodiacs. Hundreds of Zodiacs full of soldiers, and big ships, lots of ships, and I believe as well submarines in the sea.”
Following a meeting of Israel’s security and diplomatic cabinet, the statement said last night: “It was agreed that the detainees would be expelled immediately - according to the procedures set by law.
“The interior minister announced that the expulsion will begin this evening, and the assessment is that it can be completed in approximately 48 hours.”
The Foreign Office said it is seeking “urgent clarification” of the situation.
Mr Hague had welcomed a statement by the United Nations Security Council calling for a “prompt, impartial, credible and transparent” investigation into the seizure of the flotilla by Israeli commandos early on Monday.
“We look to Israel to co-operate to implement that resolution with a transparent and thorough investigation,” he said.
After a meeting of the National Security Council at the Prime Minister’s country residence at Chequers, Mr Hague said one individual had been deported while the rest were being seen by British consular officials.
As the Foreign Office confirmed that 29 of the Britons had received a visit - with no complaints about their treatment - the Foreign Secretary said he expected the detained British nationals to be deported by Israel “very quickly”.
The Israeli authorities said 50 of the 679 activists taken off the flotilla had already been taken to Israel’s international airport for deportation.
The rest were being held at the Be’er Sheva detention centre in southern Israel, having refused to identify themselves.
Mark Regev, spokesman for Israeli prime minister Benjamin Netanyahu, said that the detainees were being treated in line with international practice.
“We are not charging them with anything, we have detained them and we will help them leave our country,” he told the BBC.
However there was anger and concern among friends and relatives in the UK who complained that they were unable to establish contact with the detainees or find out what was happening to them.
Rachel Bridgeland, whose partner, Peter Venner, 63, from Ryde, Isle of Wight, was on the Turkish aid ship the Mavi Marmara, said that the Government should be putting more pressure on Israel.
“It’s absolutely terrible not knowing what has happened to him and it’s terrible that the British Government hasn’t done more, but they don’t want to fall out with Israel,” she said.
“They should insist that the British people are allowed to phone us, they have done nothing illegal.”
The British detainees were also thought to include Sarah Colborne, campaign and operations director for the Palestine Solidarity Campaign (PSC).
PSC general secretary Betty Hunter said there was no justification for their detention.
“Those held illegally by the Israeli government have committed no crime, they have simply attempted to avert a humanitarian disaster by bringing much-needed medical supplies into Gaza,” she said.
Deputy Prime Minister Nick Clegg said that the incident underlined the need for Israeli to lift its “unjustifiable and untenable” blockade of the Hamas-controlled Gaza Strip.
“What is going on in Gaza has become a humanitarian catastrophe,” he said.
“Whilst, of course, Israel has every right to defend itself and its citizens from any attack, it must now move towards lifting the blockade in Gaza as soon as possible.”
After the killing of civilian activists on board the Mavi Marmara - one of six ships in the flotilla - drew worldwide condemnation, Israel signalled there may be a temporary easing of the Gaza blockade.
An Israeli official said there is an “ongoing dialogue” with the international community on how to expand the amount of goods entering the area.
Egypt said it was freely opening its border with Gaza for the first time in more than a year to allow in humanitarian aid, setting off a rush to the crossing by thousands of residents.
Yesterday’s UN Security Council statement was finally agreed after the United States - Israel’s strongest ally - successfully watered down an earlier wording which called for the Israeli action to be condemned “in the strongest terms”.
It was followed by a statement from Nato Secretary General Anders Fogh Rasmussen who backed the call for an investigation and urged the “immediate release” of the ships and individuals being held by Israel.
Some of the harshest criticism came from Turkey, previously seen as Israel’s main ally in the Muslim world. Many of the activists on the ships - including a number of the dead - were Turkish.
Turkish foreign minister Ahmet Davutoglu described the action as an act of “banditry and piracy” on the high seas and “murder conducted by a state”.
Israel said its troops had been left with no choice after they came under attack from activists armed with knives and iron bars when they were dropped by helicopter on to the ship.
Israel ordered the families of its embassy staff in Turkey to leave the country in the wake of international outrage over its raid on the flotilla, it was reported.
Israeli media said the diplomatic mission will remain in Turkey.
A spokesman for the Israeli foreign ministry would neither confirm nor deny the reports.
Deputy Prime Minister Nick Clegg, who was a vocal campaigner against the Gaza blockade as Liberal Democrat leader before joining the Government, said the deadly incident had reinforced his view.
He told BBC Radio 4’s Today programme that Israel had “every right” to protect its people from terrorist threat.
“However, is it in Israel’s long-term security interest to have so many people confined in that way? No, I don’t think it is and what I ask my Israeli friends and Israeli politicians and officials I meet is: what’s the strategy, where do you go next, how are you going to secure in the long term, not just day to day, the security which you rightly crave?”
He added: “It (the blockade) is an absolute humanitarian catastrophe, and we should acknowledge it as such, but it is also not in Israel’s own long-term self-interest.
“So the events of the last 24/48 hours confirm in my mind, as they do if you hear what William Hague and David Cameron have done and everyone in Government, the view that the blockade on Gaza is neither sustainable nor tenable in its present form.”
A Foreign Office spokesman said that “several” of the detained Britons had agreed to be deported back to the UK, and they would be sent out of the country today.
Staff are “seeking clarification” about what will happen to those who do not agree to leave Israel, but it is understood that they will be deported without consent, he said.