Some 40 Israelis on board a Turkish Airlines flight from Tel Aviv to Istanbul were separated from the rest of the passengers upon arrival in Turkey on Monday and were questioned at length by Turkish police, marking a highly unusual event against the backdrop of a deepening diplomatic crisis between Turkey and Israel.

Whats next for Israel and Turkey after their trade of accusations over airport humiliation? Visit Haaretz.com on Facebook and answer our poll.

Open gallery view Turkish Airlines plane Credit: AP

Turkish police took the Israelis' passports upon arrival and questioned each person individually in an investigations room. Only after prolonged questioning did the Israelis receive their passports back and were freed to go.

Several passengers on a different flight that passed through Turkey on its way to Israel from Thailand told Army Radio that they were also treated in a humiliating manner at the Istanbul airport.

"They made me undress to only my underwear. A woman officer did it, but she wasn't particularly gentle. It reminded me of stories my grandma told me of her past," Alina, one of the passengers recounted.

"After the examination, she threw my clothes to the side and told me to get dressed. I was escorted out of the room and then we were told we cannot sit down – they made us stand in the corner without allowing us to use the restroom. We did not have our passports and we had no idea what is happening.

Foreign Ministry officials said in response that the event is highly unusual and serious, and said that many of the Israeli passengers called the Foreign Ministry and said they felt fear during the questioning. The Foreign Ministry turned to the Turkish Foreign Ministry and demanded an explanation, however the Turks said they were not familiar with the incident.

"At this time it looks like a local initiative of police in Istanbul, but we are still looking in to the event and mostly trying to understand what was the character of the investigation," said a Foreign Ministry official.

Officials in Ankara said in response that Turkish tourists were harassed in Israel's Ben-Gurion International Airport on Sunday evening, hours before the incident at Istanbul's airport the next morning.

A group of Turkish tourists, who arrived in Israel for the holiday of Ramadan and visited Jerusalem, said that when they arrived at the airport, Israeli security personnel delayed them for several hours and ask them for personal details, including their phone numbers, email addresses, and marital status.

"They checked our luggage numerous times and later conducted a full body search. They made us undress to our underwear and also patted down all the women in separate rooms – only the Turkish passengers underwent such an examination," said one of the tourists.

According to the passengers, their flight was delayed due to the prolonged examination of the Turkish tourists' luggage, and the group's guide said that Turkish tourists were treated differently by Israeli security officials than the other tourists.

The Israel Airports Authority said in response that they are unaware of any out of the ordinary security checks that were carried out on the Turkish passenger

The recent crisis in Israel-Turkey relations deepened after the UN-commissioned report on the 2010 Gaza flotilla raid was leaked to the New York Times, foiling a last-ditch effort to patch up relations between the two countries. Turkey then announced a series of measures against Israel, beginning with the expulsion of the Israeli ambassador and the downgrading of bilateral relations to the level of second secretary.