Some activists were barred from entering the country for refusing to promise not to engage in disorderly conduct, but Israel did allow some other activists to enter, Israeli officials said.
By Sunday night, 60 activists had been refused entry at the airport, Israeli police spokesman Micky Rosenfeld said.
Nine protesters were arrested for attempting to disrupt order at the airport, Rosenfeld said. He said there were 500 police officials there.
Mazin Qumsiyeh, a spokesman for the "Welcome to Palestine" campaign, said that more than 1,000 uniformed and plain clothes security officers were at the airport, in what he called a sign of "unprecedented Israeli hysteria and paranoia." Authorities "violently arrested" the nine activists, he said.
Activists who were sent home were being given a letter sarcastically thanking them for "choosing to make Israel the object of your humanitarian concerns."
The letter says protesters could have focused on "the Syrian regime's daily savagery against its own people," or the actions of Iran or Hamas, but instead "chose to protest against Israel, the Middle East's sole democracy," according to a copy posted on Twitter by Ofir Gendelman, a spokesman for Prime Minister Benjamin Netanyahu.
"We therefore suggest that you first solve the real problems of the region, and then come back and share with us your experience. Have a nice flight," the letter says.
Organizers of the "fly-in" event said some 1,500 to 2,000 activists mainly from Europe, the United States, and Canada would board civilian flights for Israel in order to make their way to various events in Bethlehem and other West Bank cities.
By Sunday night, only three activists who flew in had made it to Bethlehem from the Tel Aviv airport, they said. Another 20 had entered a few days before after crossing a land bridge between Jordan and Israel.
One of the activists who made it through said 27 other people who had flown with her from Lyon, France, had been detained. The woman, a French citizen named Tanya, declined to provide her last name because she said she feared repercussions from the authorities.
Activists told reporters Sunday that the event would be a success, no matter how many people participated.
"Our success is measured in terms of the media publicity the Welcome to Palestine campaign made in shedding light on the true fate of Israel's dictatorship and apartheid," organizer Abdel Fatah Abu Srour said.
Another organizer criticized Israel's letter.
"I tell Israel they are contradicting themselves about their so-called democracy when they are deporting and detaining people who are coming to visit Palestinians," said Amira Mussalam.
Activists said they were trying to draw attention to what they claim are prejudicial Israeli border policies that force many international visitors coming to Palestinian areas to lie about their destinations.
"We believe, like prisoners in prisons, we are entitled to receive visitors and Palestinians under Israeli occupation are also entitled to receive visitors," Qumsiyeh said. "So we are entitled to get international visitors to come and visit and show solidarity with us to learn about the situation, but Israel chooses to prevent these people from coming."
On Sunday, he said a number of activists had reached the West Bank, but did not say how many.
The activists who were denied entry on Sunday were from Portugal, Canada, Switzerland, France, Spain and Italy, said population and migration authority spokeswoman Sabin Hadad.
Last year, organizers staged a similar event and Israel authorities detained and deported dozens of activists who entered the country.
On Tuesday, Israel's public security minister, Yitzhak Aharonovitch called activists "provocateurs" and told Israeli news portal Ynet that they would "be dealt with in a determined and quick way," adding that "If they arrive in Israel they will be identified, removed from the plane, their entry into Israel will be prevented and they will be moved to a detention facility until they are flown out of Israel."
To that end, Israeli officials have been in touch with airlines and provided them with lists of people who are forbidden from entering the country.
"Usually airlines don't allow these people to embark, because then they have to cover the expense of the return flight," said Israeli Foreign Ministry spokesman Yigal Palmor.
"What we did last year is we had a list of number of people who have been banned from entering the country in the past, and others who will be banned now because they have openly declared that they will come here to disturb public order in one way or another," Palmor said.
Palmor said arriving passengers who are denied an entrance visa have the right to appeal but could face three days in detention before their hearing.
On Sunday, one activist in the United Kingdom said she was in a group of 30 passengers who were blocked from boarding a flight from Manchester to Tel Aviv.
"Israel was able to stop us, British passport-holders, and Israel has the power to extend its apartheid to other countries and borders," activist Norma Turner said.
Qumsiyeh insists the event is entirely peaceful in nature and suggested that Israeli authorities were over-reacting.
"The Israeli internal security is paranoid and is turning the airport into a military camp. They want to arrest the activists and are calling us provocateurs and demonstrators as they always do" Qumsiyeh said. "The activists are coming peacefully and will visit the West Bank and help us build a community school and then they will go home with no problems, Israel is creating the problems and not us."
