Two passengers with Israeli documents left an Aegean Airlines flight after other Israelis protested about their presence, the company has said.

Israeli media identified the two as an Israeli-Arab and a Palestinian, and said the protesting passengers were Jewish. The incident occurred on Sunday night, delaying the flight from Athens to Tel Aviv by more than 90 minutes.

Aegean said: “An initially small group of passengers very vocally and persistently asked for two other Israeli passengers to be checked for security issues.”

The airline said one of the men held an Israeli passport and the other had a valid Israeli residence permit. It did not mention their ethnicity.

“While it is indeed unfortunate that they were possibly racially profiling the customers, indeed their fellow Israelis … safety must be first,” the company said.

By the time the police arrived to check the two passengers’ passports, finding nothing suspicious, the outcry had spread.

“It started with three or four people and by the end there were 60-70 people standing up, demanding that the pair disembark,” a company spokesperson said. “The pilot said anyone who does not feel safe to fly should disembark and would not be compensated. But by that stage, the two men were in a poor state and wanted to leave themselves.”

Aegean said it had offered the pair overnight stay and transport on Tuesday. They were compensated for the incident and flew to Israel on an El Al flight on Monday.

“We thank again the two Israeli passengers that agreed to disembark for their understanding and collaboration and we apologise for the whole episode which was indeed extremely unfortunate,” the airline added.