Aljazeera's Gaza correspondent said the Palestinian officials were forced to return from the talks in military vehicles and others returned on foot as their vehicle had been damaged during the meeting.
Windows were smashed and tyres slashed, he said.
The meeting held between Israeli and Palestinian field leaders on Wednesday discussed the deployment of Palestinian security forces, identifying their positions, numbers and type of weapons allowed.
The Israeli delegation agreed to offer safety measures at Abu Huli military crossing and Rafah crossing.
Witnesses said Palestinian security forces began deploying last week in southern Gaza in an attempt to end the firing of rockets by Palestinian resistance groups, under orders from newly elected leader Mahmud Abbas.
They said about 20 officers had taken up positions at the Tufah crossing near a Jewish settlement bloc.
Palestinian police fanned out in north Gaza with the Israeli army's agreement, ushering in a calm that Abbas now wants to establish in the south of the territory as well.