Israeli forces clashed with Muslim protestors on Sunday at a flashpoint Jerusalem Old City, police said.

The tensions and the Jewish pilgrimage to the highly sensitive Al Aqsa mosque compound, known to Jews as the Temple Mount, were condemned by the Palestinians.

Israel's right-wing nationalist Prime Minister Naftali Bennett stood by the state's decision to allow Jews to visit the site.

According to police, in the early hours of the morning Palestinian "youths began throwing stones at the Haram Al Sharif towards police, who dispersed them". There were no official reports of arrests or injuries.

The EU delegation to the Palestinian territories in a tweet said it was "concerned over ongoing tensions" and urged that there be no "acts of incitement".

It also called for respect for the site's status quo and urged Israeli, religious and community leaders to urgently "calm down this explosive situation".

The incident took place on the Jewish festival of Tisha B'av, marking the day of the year thousands of years ago when, according to tradition, both Jewish temples located on the Temple Mount were destroyed.

The holy site lies in East Jerusalem, which Israel occupied and annexed in 1967, but is administered by the Muslim Waqf organisation which reluctantly grants Jews limited access.

A spokesman for a Jewish group encouraging such visits told AFP that 1,679 pilgrims were at the mosque compound during Sunday morning and afternoon.

The Waqf condemned the "violations and attacks" carried out by "Jewish fanatic groups, with the support and political cover of the Israeli government," it said in a statement carried by official Palestinian website Wafa, claiming Israel was "aiming for a religious war".

And the Palestinian Authority accused Israel of "tampering with the security and stability of the region" by enabling the "incursions" of worshippers.

Newly sworn-in Premier Bennett, who is from Israel's religious right but heads a coalition including leftist and Islamist parties, said he had "instructed that the organised and safe visits by Jews to the Temple Mount continue, while maintaining order at the site".

In a second statement following the Waqf and PA condemnations, Bennett stressed that "freedom of worship on the Temple Mount will be fully preserved for Muslims as well", pointing to the upcoming festival of Eid al Adha.

Two years ago, when the Jewish and Muslim holidays coincided, violence at the site left dozens of Palestinians wounded and led to seven arrests.