A spokesman for Binyamin Netanyahu, the Israeli prime minister, said earlier on Tuesday that all of the activists "would be deported immediately".
There are believed to have been a total of 682 people from 35 countries on the flotilla.
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.
Sherine Tadros, Al Jazeera's correspondent reporting from Beersheva in southern Israel, later said 500 more detainees had left the Ela Prison and would be deported.
Tadros said only about 30 activists were still in the prison.
She said that while nine people have been confirmed killed, no information had been made public about their identities.
The activists were killed when Israeli troops, using helicopters and 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.
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.
"The Israeli assault took those of us on the ship by complete surprise. We saw about 30 war vessels surrounding this ship, and helicopters attacking with very luminous bombs."
Mohamed Vall, freed Al Jazeera reporter
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.
"More troops came and immediately opened fire, and killed people on the ship without any distinction."
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".
This drew a sharp response from Israel, which said its foreign minister had complained in a telephone call to Ban Ki-moon, the UN secretary-general, that it was condemned unfairly for "defensive actions".
Turkey has warned it will cut off diplomatic ties with Israel if its citizens killed and injured in the Gaza flotilla raid are not returned by Wednesday night.
Ahmet Davutoglu, Turkey's foreign minister, also called for an international commission into the raid on the convoy which left four Turks dead.
"We have clearly stated that we would review our ties with Israel if all Turks not released by the end of the day," said Davutoglu.
Turkey has sent three planes to retrieve its nationals from Israel.
There were signs, however, that the long-term relationship Israel has had with Ankara would endure.
Ehud Barak, Israel's defence minister, spoke to Vecdi Gonul, his Turkish counterpart, on Tuesday, defence officials said on condition of anonymity.
The officials said the two men agreed the raid would not affect weapons deals, among them a planned delivery to Turkey of $183m in Israeli drones this summer.
Another aid ship
Amid the international condemnation, Egypt said it was opening the Rafah border it shares with Gaza, 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.
Abbas meanwhile criticised Israel's actions as being "stupid, terrorist and ugly".
Speaking in Bethlehem, Abbas said that "the way to seek peace has to start by Israel lifting the siege on Gaza, freezing all settlements without preconditions, and the recognition of international references".
But Israel remains defiant and said that 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.
"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."
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, saying that 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.