"This morning passengers for an easyJet flight were prevented from embarking," airport spokeswoman Aline Yazgin told AFP, adding she did not know why they had been prevented from boarding.
She said that as a result several people belongiong to a French group of pro-Palestinians had tried to get past airport security doors, resulting in authorities temporarily shutting down boarding areas.
"Around 6:00 am (0400 GMT) we shut down the security areas. We opened them again at around 6:45 am," she said. "This caused operational delays."
Organisers of the "Welcome to Palestine" campaign, which some have called the "flytilla," had said up to 800 activists were to fly in to Tel Aviv's Ben Gurion airport on Friday from various airports in a peaceful mission to visit Palestinian families.
Israel has been attempting to prevent the activists from arriving.
"Israel has given airlines a list of 342 unwanted people, warning them that they will be immediately turned back at the expense of the companies," Israeli immigration spokeswoman Sabine Hadad told AFP Friday.
Following the warning, "the companies have already refused to take on board around 200 of these passengers," she said, adding two US activists who arrived overnight were sent back to the United States.
Israel appeared to be gearing up for a confrontation, with hundreds of police at the airport near Tel Aviv, but no incidents have been reported so far on Friday.