"There are only two who are still being detained," interior ministry spokeswoman Sabine Hadad told AFP, adding that both were women. "One of them will be expelled on Thursday during the day, while the other one, who has launched a legal proceeding challenging her expulsion, will remain in detention," she said.
The activists are among around 800 people who planned to fly to Israel from Europe and the United States and head to the Palestinian territories to stay with local families as part of the "Welcome to Palestine" campaign.
Israel worked to prevent the activists from arriving by notifying airlines that certain ticket-holders would not be admitted to the country and should be denied permission to board flights.
Of those who managed to arrive, 120 were denied entry and taken into custody, pending deportation.
On Wednesday, an Israeli court ruled that two activists, who challenged their deportation, could be released if they signed pledges not to venture into certain areas without Israeli military permission.
"Yesterday's case was actually a partial victory for us because the judge ruled to release them and said that there was no reason for the government to deport them or to hold them," said "Welcome to Palestine" spokesman Mazin Qumsiyeh.
"The only conditions made on this release is that these activists should ask the Israelis for permission if they want to go to certain areas in the West Bank, like where demonstrations might happen," he told AFP.
Qumsiyeh disputed Hadad's figures for the number of activists still in Israeli detention, saying lawyers for the "Welcome to Palestine" initiative, and counts of delegation lists put the figure at around 40-50.
"That's our estimate based on what our lawyers are telling us. When the delegations were sent we received lists of who was coming and we know who was able to arrive, so we have calculated the people who are still unaccounted for," he said.
Qumsiyeh said several other activists had challenged their deportations, including a German woman whose case was to be heard on Thursday.
The "Welcome to Palestine" campaign -- dubbed a "flytilla" -- took place as a flotilla of ships trying to break a blockade on the Gaza Strip was prevented from leaving Greece. Organisers said there were no links between the two, but Israel pledged to prevent both campaigns from going ahead.