The unrest escalated already heightened tensions over the hunger strike, which has prompted anti-Israel protests across the West Bank in recent days.
In unrest in the northern West Bank town of Huwara, about 200 youths hurled rocks and exploding fireworks at soldiers, who fired back tear gas and sound bombs. During the clashes, a Palestinian speeding on a motorbike knocked over a soldier. The army said he was lightly injured.
Much of the attention has surrounded prisoner Samer Issawi, whose health has severely deteriorated after an on-again, off-again hunger strike stretching more than 200 days.
Issawi, 35, suffered a new setback on Tuesday when a Jerusalem judge rejected his request to be freed on bail. Issawi is set to be sentenced this month for violating the terms of an earlier release from prison.
Later Tuesday, U.N. Secretary-General Ban Ki-moon urged a swift solution to resolve the plight of Palestinian prisoners who are on hunger strike. U.N. spokesman Martin Nesirky said Ban was deeply concerned about the rapidly deteriorating condition of the hunger strikers, especially Issawi.
Israel is holding some 4,500 Palestinians for charges ranging from throwing stones to undertaking deadly militant attacks. Their incarceration is an emotional issue for Palestinians, who see them as heroes of their struggle for liberation from Israeli occupation. Virtually every Palestinian knows someone who has served time in an Israeli prison.
Issawi and another hunger striker, Ayman Sharawneh, were prisoners who were freed as part of a 2011 exchange that released hundreds of Palestinians, many of them militants involved in deadly attacks, in exchange for an Israeli soldier held by Hamas-backed militants.
Israel's prison service said Issawi served six years of a 26-year sentence for militant activity. Israel says he was arrested in July for violating the terms of his release by leaving his Jerusalem home and entering the West Bank three times.
He was convicted this month for violating the terms of his release, and for pressuring an eyewitness to lie to interrogators about his location, said lawyer Andre Rosenthal. He is expected to be sentenced later this month, Rosenthal said.
Issawi was hospitalized over the weekend after he lost consciousness, but his lawyers say his condition improved after receiving an IV drip containing vitamins and minerals.
Sharawneh has refused food for more than 70 days. He halted his strike for a month and resumed it two weeks ago. Sharawneh, who was arrested in January 2012, has not been sentenced.
Israel's high court is expected to hear Sharawneh's appeal on Feb. 20. There were no details on the original accusations against Sharawneh or how he had violated the terms of his release.
The other two hunger strikers are being held on administrative detention, a system where prisoners can be held without being charged for months at a time.
Amani Srahna of the Palestinian Prisoners Club, a group representing the interests of Palestinians held by Israel, said 800 inmates in three prisons were participating in Tuesday's one-day hunger protest. The prisoners include those belonging to the militant Islamic Jihad faction, which has led previous mass hunger strikes.
In the West Bank, dozens of youths, their faces masked, others with the colorful red-green-white-and black Palestinian flag tied around their necks, set tires alight, threw rocks and hurled others with slingshots at Israeli forces at the Ofer military prison near the city of Ramallah.
Soldiers fired tear gas, stun grenades and rubber bullets in response, the army said.
Six youths were moderately injured by rubber bullets and live fire, said Palestinian health official Ahmed Beitwai. The military said Israeli forces did not use live fire against the demonstrators.
In Ramallah, men and women held signs calling for the release of prisoners.
It was the second consecutive day of protests across the West Bank.
Last year hundreds of Palestinian prisoners went on a mass hunger strike to demand better incarceration conditions. In a deal mediated by Egyptian officials, they were promised more family visits and limits on administrative detention.
With additional reporting by Diaa Hadid and Ian Deitch in Jerusalem and Dalia Nammari in Ramallah.