The expulsions would be carried out by Thursday, according to Israeli military radio.
Following the deadly raid on the six-ship flotilla, Israel has deported dozens of the 682 activists from 42 countries but has been holding hundreds of others, most of them Turkish nationals.
Forty-five agreed to be deported immediately and were flown out on Monday and Tuesday, immigration police spokeswoman Sabine Haddad said earlier, adding that more than 120 Arab nationals were taken to the Jordanian border.
Hundreds of others apparently refused a demand they sign a document saying they entered Israel illegally even though the ships were seized in international waters.
The Red Cross said meanwhile it was granted access to the detainees.
"Our priority now is to check on the condition and whereabouts of the people wounded and of those detained by the Israeli authorities," said Pierre Wettach, head of delegation of the International Committee of the Red Cross.
Israel's decision to back down and release the detainees followed two days of stinging international criticism.
Despite this, the White House declined on Tuesday to specifically condemn Israel, instead saying it showed Middle East peace moves were now needed "more than ever."
US Secretary of State Hillary Clinton said later the situation in Gaza was "unsustainable and unacceptable."
"Israel's legitimate security needs must be met just as the Palestinians' legitimate needs for sustained humanitarian assistance and regular access for reconstruction materials must also be ensured," Clinton said.
She added Washington backed an Israeli probe of the raid, but stressed it must be "prompt, impartial, credible and transparent."
Israel insists the boarding would have been peaceful if the commandos had not been attacked by dozens of club-wielding activists on the Turkish ferry Mavi Marmara, which carried most of the passengers.
And a senior official made it clear Israel would not tolerate more attempts to breach its blockade of Hamas-run Gaza.
But organisers insisted they would push ahead with a fresh bid to break the blockade in the coming days.
"We knew what the risk would be and we will continue to run these flotillas," said Greta Berlin of the Free Gaza Movement.
"The Rachel Corrie will probably be there within the week," she said, referring to an aid-laden cargo ship which is currently just to the east of Italy.
The activist Berlin said organisers were working on plans for a new flotilla which would leave for Gaza in July.
But Israel was adamant it would not let any ships through.
"We will not let any ships reach Gaza and supply what has become a terrorist base threatening the heart of Israel," deputy defence minister Matan Vilnai told public radio.
As Israel and those behind the aid flotilla continued to trade blame, the UN Security Council condemned the storming of the fleet, and called for a "credible and transparent" investigation.
It also demanded the immediate release of all ships and detained civilians.
Turkish Prime Minister Recep Tayyip Erdogan called for Israel to be punished for its "bloody massacre" and urged international sanctions against its "lawlessness."
Brazilian President Luiz Inacio Lula da Silva said Israel "did not have the right" to raid the fleet in international waters, Cuba denounced the "criminal attack," and Venezuela's President Hugo Chavez condemned the "brutal massacre."
Israel blamed the activists for the confrontation, but passengers had an entirely different story.
"Personally I saw two and a half wooden batons that were used... There was really nothing else. We never saw any knives," former MP Norman Paech, 72, wrapped in a blue blanket, said on his arrival back in Berlin.
"This was a clear act of piracy," he added.
Netanyahu, who consulted with his security cabinet after calling off White House talks with US President Barack Obama, insisted the commandos had "defended themselves from a lynching."
But Israel's press was scathing about the botched operation which sparked a welter of criticism over the failure by the political and military echelons to anticipate such a scenario.
Israeli authorities said meanwhile some of the fleet's supplies were trucked to Gaza and more would follow.
Flotilla organisers said the ships carried some 10,000 tonnes of aid destined for Gaza, which has suffered a crippling blockade imposed by Israel in 2006 that Egypt has largely backed.