Israel is transferring a group of about 150 Fatah supporters from Gaza to the West Bank, reversing a decision to return them to Hamas-ruled territory.
The Israeli government says the men's lives would be in danger in Gaza.
About 180 pro-Fatah Palestinians fled Gaza to escape factional fighting Israel returns pro-Fatah members ...
Hamas arrests Fatah leaders in Gaza ...
Egypt to facilitate Hamas-Fatah talks: Abbas ...
Gaza militants fire rocket into southern Israel ...
Israel minister says too soon to talk of Gaza truce deal ... which left 11 dead. On Sunday, 30 were sent back and were detained by Hamas police.
Palestinian Authority President Mahmoud Abbas had wanted the men to return to Gaza, to keep a Fatah presence there.
In a statement, the Israeli army said it had halted the process of returning the men to Gaza after receiving information that the first returned group had been arrested and that "their lives were in immediate danger".
The detained men were reported to be members of a Fatah-affiliated clan that Hamas, which controls the Gaza Strip, blames for a recent bomb attack in Gaza.
Twenty-two of those who crossed the border into Israel were taken to hospitals for medical treatment, Israel's military said.
Israel opened the border from Gaza after both Egypt and President Abbas asked for the men to be allowed in.
Ziad Abu Sammak, one of the injured men being treated in an Israeli hospital, said it was his duty to go back to Gaza.
"We won't give up Gaza - our families and children are there," he told the BBC.
"Of course we are all scared because Hamas is using military rule not democratic rule. Anyone who is not from Hamas might be beaten, or his house destroyed, or even killed."
Accusations
In the worst factional fighting in Gaza for more than a year, 11 people were killed and 90 injured as Hamas gunmen besieged the built-up neighbourhood of the Fatah-affiliated clan, reports the BBC's Aleem Maqbool from Ramallah.
The Fatah men - some of whom were injured - ran to the border crossing where an Israeli army spokesman said some had laid down their weapons.
When Israeli soldiers went to open the fence, they came under heavy fire, presumably by Hamas, the spokesman said.
The Fatah supporters were handcuffed and stripped for security screening as they crossed into Israel.
Fatah and Hamas blamed each other for starting the fighting on Saturday.
Hamas had accused Fatah supporters of involvement in a bombing on 25 July that killed five Hamas members and a young girl.
Hamas fighters had tried to storm the family home of the Hilles clan in Gaza City on Saturday morning, using grenades and mortars, reports say.
A spokesman for the Hamas-run interior ministry accused the clan of hiding bombing suspects in its compound.
"The Hilles family has become a military force and members of the family have been attacking, abducting and even killing people," spokesman Ehab al-Ghasin said.
The family denied the accusation.
(BBC)
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