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Hamas sources told Ynet that some of the group members were arrested upon their return, but their number and identity was unclear.
Hamas security forces set up a barrier on the road leading from the Nahal Oz crossing into Gaza City, where the Fatah men were arrested. Another group remains on the Palestinian side of the crossing and has yet to enter the Strip.
Organization sources said the Palestinians arrested were taken in for questioning and "would not undergo any type of flamboyant revenge."
Security sources told Ynet on Sunday that 32 of the residents were returned to Gaza by the early morning hours. The rest will be sent back later in the day or on Monday.
Dozens of Palestinians still hospitalized in Israel will be returned the Strip when their medical condition allows it.
The sources said that the decision to return the Palestinians to Gaza was made following an agreement reached between Defense Minister Ehud Barak and Palestinian President Mahmoud Abbas. Palestinian officials have yet to comment on the agreement.
Hamas' media outlets reported that Abbas and Israel were not interested in some of the Fatah members who fled to Israel. PA officials said that the Palestinian leadership in Ramallah was displeased with the Fatah men's escape from the Strip and that the return of another group to Gaza would be considered in the coming days.
"We are against emigration within the PA territories, regardless of its reasons," a PA official said.
Israeli security sources expressed their objection to the transfer of the Fatah men to the West Bank, explaining that these were people who were involved in terror activities against Israel in the past and that such a move would harm Israel's defense interests.
Hamas waits for returning Fatah men in Gaza (Photo: AFP)
Northern Gaza Brigade Commander Colonel Ron Ashrov told Ynet on Saturday night that IDF forces rescued dozens of Fatah members who were fleeing Gaza City under heavy machine gun, sniper and mortar fire.
At around 5 pm, following the surrender of the Fatah-affiliated Hilles clan to Hamas security forces in Gaza City, dozens of fleeing clan members began making their way toward the Gaza-Israel border, where they were rescued by IDF forces and taken into Israel.
A total of 188 Palestinians were allowed entry into the country following the fierce clashes with Hamas, which left nine people dead and more than 80 wounded.
The rescue was authorized by Defense Minister Barak at the request of Palestinian President Abbas and senior Egyptian officials.
Most of the Palestinians who entered Israel are temporarily being held in IDF bases near Gaza. They were interrogated overnight in order to ensure that they are not hostile elements.
Twenty-two of the Palestinians who entered Israel were injured during the clashes. Five of them were taken to the Soroka Medical Center in Beersheba for treatment. One of the Palestinians was reportedly in serious condition, while the other two sustained moderate and light wounds.
Ten more Palestinians were taken to the Barzilai Medical Center in Ashkelon; one of them was listed in serious condition, and the rest suffered moderate and light wounds.
The Gaza clashes broke out on the backdrop of the high tension between the rival Palestinian factions in Gaza, following an explosion which killed five Hamas members and a Palestinian girl about a week ago.
Hanan Greenberg contributed to this report