At least five people were injured as Palestinian protesters clashed with Israeli Defence Forces (IDF) outside the Ofer Prison near the West Bank city of Ramallah.
About 200 demonstrators gathered in front of the military detention facility to demand the release of Palestinian prisoners form Israeli jails.
The protest came after the Israeli government backtracked on its pledge to free 26 Palestinians as part of peace negotiations with the Palestinian authority.
Demonstrators set tires alight and threw stones at security forces, which responded by firing tear gas, stun grenades and rubber bullets.
Israel said five Palestinians were wounded, while Palestinian news agency Ma'an put the toll at 13, including four people it said were hit by live bullets.
Another protest was staged in front of an Israeli checkpoint in the West Bank town of Bethlehem.
Tension has been rising in the West Bank, as the US-brokered peace talks that were re-launched after years of inaction last summer seem on the brink of collapse.
Israel and the Palestinian authority blame each other for the crisis, which has now been blamed on both parties by US Secretary of State John Kerry.
Earlier this week Israel's chief negotiator with the Palestinians, Tzipi Livni, confirmed the government would not release a fourth batch of Palestinian prisoners, as earlier promised, saying the decision was in response to a surprise bid by Palestinian president Mahmoud Abbas bid to sign more than a dozen international conventions.
However, Abbas said he signed letters of accessions to 15 international conventions, thus bolstering Palestine claims to statehood, in response to Israel's failure to release the prisoners.
Kerry said that both sides had taken "unhelpful, unilateral actions".
"This is not an open-ended effort, it never has been," Kerry said. "It is reality check time, and we intend to evaluate precisely what the next steps will be."
"Both parties say they want to continue, neither party has said they want to call it off, but we're not going to sit there indefinitely," he said.