The Israeli government has deported to Jordan more than 100 activists seized from the Gaza aid flotilla, and has promised to release the rest of the detainees within 48 hours.

Those freed were mostly from Arab countries and were driven by buses across the Allenby Bridge into Jordan on Wednesday.

A spokesman for Binyamin Netanyahu, the Israeli prime minister, said earlier on Tuesday that all of the activists - a total of 682 people from 35 countries – "would be deported immediately".

Al Jazeera's Nisreen El-Shamayleh, reporting from the Allenby Bridge, said the deported passengers were from a dozen countries, most without diplomatic relations with Israel. Several Al Jazeera employees were among the group.

Nine activists were believed to have been killed when Israeli troops, using helicopters and fast dinghies, stormed the Mavi Marmara, the lead vessel of the six-ship convoy dubbed the Freedom Flotilla, on Monday.

The military said it opened fire in self defence when it encountered resistance from activists wielding metal rods and chairs, and released pictures which appeared to show a handful of soldiers being beaten and clubbed by dozens of activists.

Guns pointed

But activists' accounts of what happened disputed the Israeli claim.

Huseyin Tokalak, the captain of one of the seized ships who was freed on Tuesday, told a news conference in Istanbul that an Israeli navy ship threatened to sink his vessel before troops boarded and trained their guns on him and his crew.

"They pointed two guns to the head of each of us," Tokalak said.

Others said that the soldiers had opened fire even after passengers had raised the white flag.

Al Jazeera's Mohamed Vall, who was on board the Mavi Marmara and was released into Jordan on Wednesday morning, said the size of the Israeli attack surprised the ship's passengers.

"The Israeli assault took those of us on the ship by complete surprise," Vall said.

"We saw about 30 war vessels surrounding this ship, and helicopters attacking with very luminous bombs."

Meanwhile, the UN Security Council has called for "a prompt, impartial, credible and transparent investigation conforming to international standards" into the Israeli raid.

It also condemned "those acts which resulted in the loss of ... civilians and many wounded", drawing a sharp response from Israel, which said its foreign minister complained in a telephone call with Ban Ki-moon, the UN secretary-general, that it was condemned unfairly for "defensive actions".

In Turkey, a visibly angry prime minister told parliamentary deputies that Israel should "definitely be punished" for its "bloody massacre" of the activists.

"The time has come for the international community to say 'enough'," said Recep Tayyip Erdogan, who demanded the immediate lifting of "the inhumane embargo on Gaza".

There were signs, however, that the long-term relationship Israel has had with Turkey – arguably its most important Muslim ally – would endure.

Ehud Barak, Israel's defence minister, spoke to his Turkish counterpart, Vecdi Gonul, on Tuesday, and they agreed the raid would not affect weapons deals – among them a planned delivery to Turkey of $183m in Israeli drones this summer - defence officials said on condition of anonymity.

Rafah border opened

Amid the international condemnation, Egypt said it was opening the Rafah border it shares with Gaza for the first time in more than a year, to allow in humanitarian aid after a request from the governing Hamas Palestinian faction.

Egypt, in co-ordination with Israel, has rarely opened the border since Hamas seized control of Gaza in 2007 from forces loyal to Mahmoud Abbas, the Palestinian president.

But Israel said it was ready to intercept another aid ship, the Rachel Corrie, that organisers of the Freedom Flotilla planned to send to the Gaza Strip next week.

Netanyahu convened his security cabinet to debate what Israeli critics called a botched raid, and ministers said the naval blockade of 1.5 million Palestinians in the Gaza Strip would continue.

"The opening of a sea route to Gaza would pose a tremendous risk to the security of our citizens. Therefore we continue a policy of a naval blockade," Netanyahu told his ministers.

Israel's security cabinet said in a statement that it "regrets the fact there were deaths in the incident, but lays full responsibility on those who took violent action that tangibly endangered the lives of Israeli soldiers".

It added: "Israel will continue to defend its citizens against the Hamas terror base," referring to Gaza.

No US condemnation

The bloodshed on Monday also put Israel's tense ties with the US under further strain and placed under scrutiny the relationship between the allies.

Al Jazeera's Anita McNaught, reporting from Istanbul, said Erdogan, in his speech, "mentioned the unmentionable, saying that Israel acts because it has powerful friends".

The US has, thus far, refused to condemn the Israeli raid, with Hillary Clinton, the US secretary of state, telling reporters in Washington DC that "the situation from our perspective is very difficult and requires careful, thoughtful responses from all concerned".

Clinton called on the Israeli government to ease the blockade of Gaza.

"The situation in Gaza is unsustainable and unacceptable. Israel's legitimate security needs must be met just as the Palestinian's legitimate needs for sustained humanitarian assistance and regular access to reconstruction materials must also be assured," she said.

In a telephone call with Erdogan, Barack Obama, the US president, expressed his condolences for those killed in the raid - four of them Turks - and reiterated US support for an impartial investigation "of the facts surrounding this tragedy", the White House said.

He also said it was important to find "better ways to provide humanitarian assistance to the people of Gaza without undermining Israel's security" the White House statement added.