Around 150 members of a Palestinian clan affiliated with Fatah wait under armed guard at the Israeli border, after running away from clashes with Hamas.
Medical officials said at least nine people had been killed in the confrontation.
The violence broke out when Hamas gunmen raided a stronghold of the Helles clan in Gaza City, searching for suspects of a deadly bombing last week.
Around 80 people, some of them children, were also wounded in the battle.
The Interior Minister of Hamas said dozens of clan members had been arrested, including some but not all of the suspected bombers.
“We stress that officials from Fatah are involved in the explosions and bombings,” he said. “They are inciting, organising and financing groups to bomb the Gaza strip.”
There were reports that Fatah’s leader President Mahmoud Abbas had called the head of the clan Ahmed Helles to express solidarity.
A six year-old girl and five Hamas militants were killed in last Friday’s beachside bombing attack.
Tit for tat Hamas and Fatah crackdowns led to hundreds of arrests.
Analysts fear the latest violence has also dealt a death blow to efforts to bring about Palestinian unity.