A 12-year-old boy was seriously wounded by soldiers firing tear gas and rubber-coated steel bullets to disperse stone-throwers in the crowd.
Protesters have focused in recent weeks on a particularly contentious section northwest of Jerusalem that would cut off eight Palestinian villages and disrupt the lives of 30,000 people.
The high court on Wednesday froze construction of that 15-mile stretch after retired Israeli army officers argued that Israel could have drawn a much less intrusive route.
Israel says it needs the barrier to stop suicide bombers who have killed more than 450 Israelis in 42 months of violence. Since September 2000, dozens of bombers have infiltrated across the "Green Line," Israel's boundary before it captured the West Bank in the 1967 Mideast war.
Palestinians object to the route of the barrier, which cuts deep into the West Bank in several places and encircles towns and villages, cutting tens of thousands of people off from their farms, services and schools.
At the Israeli Supreme Court, a group of retired Israeli security officers joined Palestinian criticism of the route and argued that the barrier will be more effective if it runs along the Green Line and does not dip into the West Bank.
"The Green Line is the shortest line, and also the one that least hurts the Arabs," said Shaul Givoli, a retired senior police commander and leader of the group, the Council for Peace and Security.
The court ordered the Israeli military to respond to the report, and extended a freeze first imposed on Feb. 29 until it hears back from the army, said attorney Mohammed Dahla, representing the Palestinian villagers.
Israel has already changed its plans several times under local and international pressure.
A senior Israeli government official said the route of the barrier might have to be altered further. "If there are places where we have to change the route of the fence, we will do this," he said, speaking on condition of anonymity.
Palestinians have also mounted a challenge to the barrier at the International Court of Justice in The Hague (news - web sites).
In Thursday's protest, hundreds of Palestinians, including many women and children, marched to one of the barrier construction sites still active, west of the frozen section.
Soldiers fired tear gas and rubber-coated steel bullets to break up people who were throwing stones. A 12-year-old boy suffered a fractured skull from a rubber bullet, hospital officials said.
While building the barrier in the West Bank, Israel is also talking of a pullout from most or all of the Gaza Strip (news - web sites). The two plans make up Prime Minister Ariel Sharon (news - web sites)'s plan for unilateral action if peace talks remain stalled.
Palestinian Prime Minister Ahmed Qureia said Thursday that the Gaza pullout could be a positive move, but under strict conditions.
Qureia said Israel must leave all of Gaza, turn over control of international borders to the Palestinians, give free passage between the West Bank and Gaza through Israel and allow an international force to patrol Gaza. Sharon has given no indication that he would agree to any of those points.
If Sharon's intention is to trade Israeli control of parts of Gaza for entrenchment in the West Bank, Qureia warned, "this will explode the situation in the area."
A suicide bombing Sunday at the Israeli seaport of Ashdod — the first time Palestinian bombers succeeded in leaving Gaza and carrying out an attack — set off an intensified Israeli campaign against militants in Gaza.
There were no reports of clashes Thursday, but a Palestinian wounded in Israeli helicopter missile strikes on Wednesday in the Rafah refugee camp died, bringing the death toll there to five. Two other Palestinians were killed in an air strike in Gaza City this week.
