A group of 188 Palestinians granted refuge in Israel amid deadly fighting between rival factions Hamas and Fatah are being returned to Gaza.
The men, members of a clan allied to Fatah, were allowed into Israel after fighting left nine dead on Saturday.
Palestinian Authority President Mahmoud Abbas, who heads Fatah, told Israel not to transfer them to the West Bank, as he had earlier requested.
Hamas said it detained 30 on return but has released all but five.
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 were taken to hospitals in Israel for medical treatment, Israel's military said.
Israel opened the border after both Egypt and President Abbas asked for the men to be allowed in.
It also agreed to an initial request by Palestinian Authority leaders to send the men to the West Bank.
However, Israel's defence ministry now says Mr Abbas has asked for the group to be sent back into Gaza.
One Fatah official, Hussein al-Shaikh, said the Palestinian Authority was discussing with Israel exactly how to return the men.
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."
In the worst factional fighting in Gaza for more than a year, nine 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.
While Hamas insists that Palestinian factional reconciliation is still possible, our correspondent says the weekend's events have put a huge strain on already bitter relations.
Hamas had accused Fatah supporters of involvement in a bombing a week ago 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.