Susan Elliott, a spokeswoman for Delta, said the letter was written to encourage the Israelis to work out these problems with the International Air Transport Association, a trade group representing 230 airlines. Steve Lott, spokesman for the association, called the program “one of the most complicated and counterintuitive systems for ensuring aircraft security.”

Approximately 30 percent of flights to Israel fly through disputed airspace that can increase the workload in the cockpit, making it more likely that pilots may err in entering the security code, according to the International Federation of Air Line Pilots’ Associations. And because it there is no set procedure for how to handle these kinds of pilot errors, critics say, flights can be put in jeopardy.

“People do shoot down airliners, sometimes on purpose,” said Gideon Ewers, a spokesman for pilots association. “Sometimes they shoot them down by mistake. Whether intentional or unintentional, things can happen.”

In addition to safety concerns, international airlines and the European Union say, the program creates logistical problems by separating pilots into those with PINs who can fly into Israel and those who cannot. The director general for the European Commission’s Air Transport Directorate, Daniel Calleja, told the Israelis this could restrict “the ability of airlines to efficiently allocate their personnel.” In a letter sent earlier this month, Mr. Calleja made a veiled threat that this could “have immediate implications on the current air services agreement between the EU and Israel.”

Mr. Ewers said another meeting was scheduled with the Ministry of Transport for later in the week where pilots would ask that the program be scrapped.

The ministry declined to answer questions about the program. But it said in an e-mail message that the security program was still in the trial phase and that a decision on whether to continue it would be made soon.

Ziad Haddad, an international airline compliance specialist, discounted the possibility that commercial airliners were threatened by the program. “I am sure that the risk factor was reduced to the minimum and the Israeli authorities have studied that thoroughly to protect against overreacting or mistakes, meaning that to enter a wrong code or data by mistake will never lead to shooting down the aircraft,” he said.

Richard Bloom, a professor and airline security expert at Embry-Riddle Aeronautical University in Prescott, Ariz., said it was possible that Israel would push back even in the face of strong opposition. “If they have validated some sort of risk that suggests, with all its superficial flaws, it is the right system, I doubt they would share it with many people,” he said.