JERUSALEM, Sept 5 (Jeffrey Heller/Reuters) - Israeli passengers said they were segregated and searched at Istanbul airport on Monday and Turkish tourists made similar complaints about treatment in Israel, accounts that further stoked a heated feud between the two countries.

Three days after Turkey expelled the Israeli ambassador over Israel's refusal to apologize for a raid that killed nine Turks on a ship trying to break its blockade of Gaza in 2010, visitors from both countries were feeling unwelcome.

Hayuta Leibovich, an Israeli who manufactures clothes in Turkey, said she and other Israelis in line at passport control at Istanbul's Ataturk airport were told by security officers to stand in a corner of the terminal.

They gathered us in a group and asked for our passports -- not very nicely, she said. I felt as if they put us in a ghetto.

Leibovich said she usually speeds through the airport's arrival procedures in about 15 minutes during her frequent business trips to Turkey.

On Friday, Turkey -- a former strategic ally of Israel and once a hugely popular vacation spot for Israelis -- froze all military pacts with Israel, kicked out its ambassador and threatened legal sanctions after a United Nations report on the 2010 incident was issued.

Israel has spurned Turkish demands to apologize for the killings, saying its commandos acted in self-defense after meeting violent resistance from pro-Palestinian activists in a flotilla challenging an Israeli naval blockade of Gaza, which is run by the Palestinian Islamist movement Hamas.

A Foreign Ministry spokesman in Jerusalem said the Israeli travelers were questioned individually and waited about 90 minutes before their passports were returned and they were released.

An Israeli woman who gave her name only as Orit said she was in transit at Istanbul airport when she and about 20 other Israelis were separated from other passengers.

They told us to stand in the corner -- to humiliate us as much as possible, she told Israel Radio.

Orit said the passengers were taken away for strip searches before being allowed to board a flight to Israel at the last minute. We were all traumatized, she said.

An Istanbul airport official said in televised remarks shown on Israeli Channel 2 that the decision to be more strict with Israeli passengers was made by the Foreign Ministry.

In accordance with reciprocity principles and following an order we received from the Foreign Ministry, we will treat Israeli nationals in the same way as Turkish nationals are treated in Israel, Ahmet Aydin said in translated remarks.

The Anatolia news agency reported that Turkish tourists arriving from Israel said they underwent body searches at Tel Aviv's Ben-Gurion airport before being given the go-ahead to leave the country.

Eyup Ansar Ugur, a Turkish guide who travelled with a group of Turkish tourists who went to Israel during the Ramadan Muslim holiday, said Turkish tourists were singled out and mistreated by Israeli officials.

There was a different treatment against Turkish people. Our luggage was rummaged by Israeli security officials many times. Since the search of our luggage took so long, our flight was delayed. They went through a napkin three times, and searched my trousers fifty times.

Another tourist, who was not identified in the report, said the Israelis treated the group as if we were terrorists.

Asked about the report, a spokesman for Israel Airports Authority gave no details about the alleged incident, saying only: Ben-Gurion security operates in accordance with security requirements and under the guidance of professional authorities.

Tourism between Israel and Turkey has declined as political tensions have risen.

In the first five months of 2011, only 30,000 Israeli tourists visited Turkey compared with 72,500 during the same period in 2010. The number of Turkish visitors to Israel fell slightly over the same periods, from around 6,900 to 6,600. (Additional reporting by Ankara bureau; Editing by Karolina Tagaris)