"A couple of Belgians were returned overnight, and 118 pro-Palestinian activists are still being held in our prisons," immigration service spokeswoman Sabine Hadad told AFP.
"We hope it will be possible to return them to their home countries in the next 48 hours. It will depend on what spaces are available on departing flights," she added.
The activists are currently being held in Beersheva's Ela prison, in southern Israel and the Guivon prison in Ramleh, near Tel Aviv.
Most of the activists being held are French, but nationals from the United States, Belgium, Bulgaria, Holland and Spain were also in detention.
The activists were participating in the "Welcome to Palestine" campaign in which up to 800 activists planned to fly into Israel and head to the Palestinian territories on a peaceful mission to visit Palestinian families.
Israeli authorities mobilised diplomatic and security forces 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 from boarding at their ports of departure.
Of those who managed to arrive, four activists from Germany and Holland were authorised to stay after giving a written commitment "not to provoke disorder" and "to avoid places of (Israeli-Palestinian) confrontation."
Israeli news website Ynet said on Saturday that around 50 European pro-Palestinian activists who managed to enter Israel despite the security procedures at Ben Gurion Airport had crossed into the West Bank.
The "Welcome to Palestine" campaign took place as a flotilla of ships trying to break a blockade on Gaza 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.