Zamir said all of the people had been taken to Ben Gurion airport or the Jordanian border.
Yehuda Weinstein, Israel's attorney general, said Israel decided not to prosecute any of them, writing in an order on Wednesday that "keeping them here would do more damage to the country's vital interests than good".
Ayman Mohyeldin, Al Jazeera's correspondent in Jerusalem, said that four Palestinian-Israelis remained in prison.
Earlier on Wednesday, more than 100 of the activists, mostly from Arab countries, were driven by buses across the Allenby Bridge into Jordan.
Eighteen Kuwaiti activists detained by Israel returned home on Wednesday, accusing Israeli troops of having opened fire without warning.
The activists were flown home aboard a government plane from Jordan after crossing the border.
"Israeli commandos started shooting from the air without warning," said Mubarak al-Mutawa, a lawyer who was on the main vessel, the Turkish-flagged Mavi Marmara.
"They killed a number of volunteers even before landing aboard the ship," he said on arrival at Kuwait Airport.
Israel says its commandos opened fire in self defence when they 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.
The UN Human Rights Council in Geneva, Switzerland, condemned Israel for its "outrageous attack".
The 47-member body passed a resolution on Wednesday establishing a factfinding mission into possible international law violations.
Authorities said 682 people from more than 30 countries had been on board the six ships that tried to break Israel's blockade of the Gaza Strip.
The activists included hundreds of Turks, four of whom were killed.
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, said 210 Turkish nationals were scheduled to be flown to Istanbul from Israel on Turkish planes, while it is believed around 20 injured people will return via Ankara, on ambulance planes.
Sherine Tadros, Al Jazeera's correspondent reporting from Beersheva in southern Israel, 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 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
Activists' accounts of what happened contradict Israeli explanations of the raid.
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.
"More troops came and immediately opened fire, and killed people on the ship without any distinction."
The UN Security Council has called for "a prompt, impartial, credible and transparent investigation conforming to international standards" into the Israeli raid.
As a new standoff with another aid ship loomed, David Cameron, the British prime minister, said Monday's pre-dawn Israeli attack was "completely unacceptable".
Israel remains defiant about the raid and says it is ready to intercept another aid ship, the Rachel Corrie, that organisers of the Freedom Flotilla planned to send to the Gaza Strip next week.
Accusing international critics of "hypocrisy," Binyamin Netanyahu, the Israeli prime minister, defended the seizure of the aid ships on Wednesday.
In a televised address to the nation, he said he would continue to blockade Gaza, saying that to lift the embargo would turn it into a base for Iranian missiles that would threaten both Israel and Europe.
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".
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.