A Palestinian has died after being shot in the head in an East Jerusalem neighbourhood near the Old City, the Palestinian health ministry said, as clashes broke out in the area.

Tensions have mounted over new security measures at a highly sensitive holy site and the police restricting access for Muslim prayers.

The ministry however did not specify who was behind the shooting in the Ras al-Amud neighbourhood.

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

In anticipation of protests on Friday, Israeli police barred men under 50 from entering the Old City for prayers, while all women were allowed in.

Police said later 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 the devices 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 the Old City found 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 50 or over would be allowed in.

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

“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 US.

“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 US and the UN Middle East envoy expressing concern.

The Palestinian president, Mahmoud Abbas, spoke with Donald Trump’s senior adviser and son-in-law, Jared Kushner.

Abbas urged the US administration to immediately intervene and warned the situation was “extremely dangerous and might spiral out of control”, the Palestinian Authority’s official Wafa news agency reported.

The Turkish president, Recep Tayyip Erdoğan, has also called on Israel to remove the detectors. He spoke by telephone with both Abbas and the Israeli president, Reuven Rivlin, on Thursday.

Israel’s 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 against the use of metal detectors.

Friday prayers draw the largest number of worshippers – typically thousands – and speculation had been mounting that Netanyahu might order the removal of the detectors.

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

Police said they had increased their deployment of officers in and around the Old City, with units “mobilised in all areas and neighbourhoods”.

The new security measures were put in place after a fatal gun and knife attack near the compound on 14 July.

Three Arab Israeli assailants fled to the compound after the attack which left two policemen dead. The three were shot dead by security forces.

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

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

It said the closure was necessary for security checks.

In the Gaza Strip, Islamist movement Hamas called for a day of “rage” on Friday. In the city of Hebron in the occupied West Bank, Palestinians also prayed outside in support of the Al Aqsa protests.

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

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