The stone-throwers broke windows and glass doors in Thursday's protest outside the hotel in the city of Ramallah before Palestinian riot police arrived.
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Organizers say the conference was cut short and three dozen Israeli participants were rushed out the back door, put on Palestinian police buses and driven to safety.
The participants are part of a group that has been regularly meeting to try to garner popular support for Israeli-Palestinian peace talks and break down barriers between the two sides.
Protesters say they object to attempts at normalizing Israeli-Palestinian relations at a time when Israel's military occupation of Palestinian lands continues.
There was no immediate report of injuries or arrests.