"Two of the activists were sent back during the night and 56 others are still in jail, but dozens are being sent home today," immigration service spokeswoman Sabine Hadad said.
"They will leave on five flights scheduled in the afternoon," she said.
The detainees were part of the "Welcome to Palestine" campaign in which up to 800 people from Europe and the United States planned to fly to Israel and head to the Palestinian territories to visit Palestinian families.
Israeli authorities used diplomatic and security means to try to head off the incoming activists.
Officials said that by notifying foreign airlines of ticket-holders who would not be admitted to Israel, they had prevented hundreds of people from boarding at their ports of departure.
Of those who managed to arrive, 120 were denied entry to Israel and taken into custody, although a handful were later admitted after signing pledges not to take part in public disorder.
The "Welcome to Palestine" campaign took place as a flotilla of ships trying to break a blockade on the Gaza Strip was prevented from leaving Greece.
The timing of the fly-in campaign led some to dub it a "flytilla," although organisers denied their mission was linked to the attempt to run the blockade.