Seventy people taking part in the "Welcome to Palestine" mission arrived to take the 6.30am (0430 GMT) flight but only 25 or 26 made it onto the plane, said group spokesman Xavier Renou at the airport.
He said some had received an email from airline easyJet a few days prior "inviting us not to come," and offering a refund but others had not been contacted.
"There were lists established, it's very likely, by Israel to give to companies and to police so they were checking our names when we arrived.
Those not allowed to board were told that as a sovereign state Israel had the right to ask companies to refuse boarding to certain people they identified, said Renou.
Geneva police, however, said only two people were prevented from boarding the flight. The protestors left the airport just before noon (1000 GMT).
The activists were part of a "flytilla" or "fly-in" being held for a third consecutive year.
Its organisers in the West Bank say they want to publicise Israel's control of movement into and out of the Palestinian territory and to express solidarity with the Palestinians.
"We didn't want to go to Israel, we wanted to go to Palestine, which is our legal right, which is a legal right protected by UN policy," said Renou.
Israel deployed hundreds of police, many of them undercover, to Ben Gurion airport outside of Tel Aviv to block the arrival of activists whom organisers predicted would number up to 1,500, more than a third of them from France.
Following Israeli warnings that airlines would have to foot the bill for the activists' immediate return, at least four European carriers -- Air France, Britain's budget carrier Jet2.com, Germany's Lufthansa and Swiss Air -- all prevented an unspecified number of passengers from flying in, European officials said.