Israeli soldiers shot and wounded five Palestinians in clashes in the West Bank on Friday, medics said, after the funeral of a man killed during an army raid.

Clashes broke out between stone-throwing Palestinians and Israeli troops at the Atara checkpoint near the town of Birzeit shortly after the funeral, and medics said five people suffered bullet wounds to the legs.

The army said some 200 Palestinians began throwing stones at Israeli forces, who used "riot dispersal means" against them, including live fire "against the main instigators."

The clashes came after Motazz Washaha was found dead in his home in Birzeit following a Thursday morning raid by the army, which said he was "suspected of terror activity."

Some 4,000 mourners attended Washaha's funeral at Birzeit, north of the West Bank administrative centre of Ramallah, calling on Palestinian factions to unite and avenge Washaha's killing.

He was identified by neighbours as a member of the leftist Popular Front for the Liberation of Palestine, and the movement's red flags were visible at the funeral.

Washaha's death came as Amnesty International criticised Israel's killing of dozens of Palestinian civilians in the occupied West Bank over the past three years.

In east Jerusalem, meanwhile, Israeli security forces clashed with stone-throwing Palestinians after the weekly Friday prayers.

Police arrested three Palestinians in Ras al-Amud, just outside the Old City, an army spokeswoman said.

Police had barred men under the age of 50 from attending prayers at the Al-Aqsa mosque compound, in order to prevent disturbance, and hundreds of Muslims prayed instead on streets adjacent to the Old City where the holy site is located.