Three Palestinians were killed and dozens wounded yesterday as clashes erupted between protesters and Israeli forces over new security measures at an ultra-sensitive Jerusalem holy site where police restricted access for Muslim prayers.

One Palestinian was shot dead by Israeli gunfire in the A-Tur neighbourhood of east Jerusalem, according to the Palestinian health ministry.

A second Palestinian was killed by gunfire in east Jerusalem's Ras al-Amud neighbourhood, while a third was shot dead in Abu Dis in the occupied West Bank, the ministry said, without providing details on the circumstances.

Israel's army confirmed it was involved in clashes in Abu Dis.

The unrest came after Israeli ministers decided not to order the removal of metal detectors erected at entrances to the Haram al-Sharif compound, known to Jews as the Temple Mount, following an attack nearby a week ago that killed two policemen. The compound contains the revered Al-Aqsa mosque.

In anticipation of protests, Israeli police yesterday barred men under 50 from entering Jerusalem's Old City for prayers, while all women were allowed in.

Police said later in the day that discretion could be applied in the use of the metal detectors instead of forcing everyone to go through them.

But Palestinian and religious leaders were still calling on worshippers not to enter until they were removed.

Hundreds held midday prayers near the gates of the Old City in protest. According to police, dozens of people entered the compound.

Crowds gathered outside Jerusalem's Old City found shops closed and streets around Damascus Gate -- the entrance most heavily used by Palestinians -- blocked.

A group of several hundred people, including Muslim leaders, marched towards the Lions Gate entrance to the mosque compound, but police informed them that only men aged 50 or over would be allowed in.

Police later fired stun grenades and tear gas towards protesters outside the Old City, while Palestinians threw stones and other objects at security forces in some areas.

The Palestinian Red Crescent reported that 109 people were wounded in Jerusalem, of whom 38 were taken to hospital. No injury toll was given for the West Bank.

Israeli forces detain a Palestinian man. Photo: AFP, Reuters

"They turned back everyone who came here to pray but then I told them I was going to the doctor, but they did not let me in," said Ulfat Hamad, 42, who was visiting from the United States.

"I am going to pray here with others," he said outside the walls.

Tensions have risen since police installed the metal detectors in a move Palestinians and other Muslims perceive as a means for Israel to assert further control over the compound containing the revered Al-Aqsa mosque and Dome of the Rock.

The controversy has resonated beyond Israel and the Palestinian territories, with the United States and the UN Middle East envoy expressing concern.

Palestinian president Mahmud Abbas spoke with US counterpart Donald Trump's senior adviser and son-in-law Jared Kushner.

He urged the US administration to immediately intervene, warning the situation was "extremely dangerous and might spiral out of control," the Palestinians' official Wafa news agency reported.

Turkish President Recep Tayyip Erdogan too has called on Israel to remove the detectors. He spoke by telephone with both Abbas and Israeli President Reuven Rivlin on Thursday.

Israeli Prime Minister Benjamin Netanyahu stressed the metal detectors were intended to ensure the safety of worshippers and visitors and not an attempt to disturb the fragile status quo under which Jordan is custodian of the site and Jewish prayer is forbidden.

Palestinians have been refusing to enter the compound all week in protest at the metal detectors.

The main weekly prayers on Fridays draw the largest number of worshippers -- typically thousands -- and speculation had been mounting that Netanyahu might order the metal detectors removed.

But after consultations with security chiefs and members of his security cabinet, Netanyahu decided not to do so.

Police said they had boosted their forces in and around the Old City, with units "mobilised in all areas and neighbourhoods".

The metal detectors were put in place following a gun and knife attack near the holy compound that killed two Israeli policemen on July 14.

Three Arab Israeli assailants fled to the compound after the attack, where they were shot dead by security forces.

Israeli police said the weapons were smuggled into the holy site which was then used as the launchpad for the attack.

Israel initially closed the compound for two days following the attack in a highly unusual move, shutting it for last Friday's prayers.

It said the closure was necessary for security checks.

Israel began reopening it on Sunday, but with metal detectors in place to prevent weapons being smuggled inside.

In the Gaza Strip, Islamist movement Hamas had called for a day of "rage" yesterday over the measures.

In the city of Hebron in the occupied West Bank, Palestinians also prayed outside in support of the Al-Aqsa protests and clashed with Israeli soldiers.

The Haram al-Sharif/Temple Mount is central to the Israeli-Palestinian conflict.

It lies in east Jerusalem, seized by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.

It is considered the third holiest site in Islam and the most sacred for Jews.