Tensions over control of the Haram al Sharif compound of mosques in Jerusalem’s Old City has reached a pitch unseen since clashes at the site sparked the second intifada nine years ago.

Ten days of intermittently bloody clashes between Palestinians and Israeli security forces in Jerusalem culminated yesterday in warnings by Palestinian officials that Israel was “sparking a fire” in the city. Israel’s Jerusalem Post newspaper similarly wondered whether a third intifada was imminent.

Israel deployed 20,000 police to safeguard the annual Jerusalem march, which was reported to have attracted a crowd of 70,000 passing through sensitive Palestinian neighbourhoods close to the Old City.

The ostensible cause of friction is Israel’s religious holidays that have brought Jewish worshippers to the Western Wall, located next to the Haram al Sharif and traditionally considered the holiest site in Judaism, believed to be the only remnant of the Jewish temple destroyed by Herod in AD70.

At a deeper level for Palestinians, however, the ease with which Jews can access sites in and around Jerusalem, while the city is off-limits to the vast majority of Palestinians, highlights the extent to which Palestinian control over Jerusalem and its holy places has been eroded by four decades of occupation.

That point was reinforced on Sunday when the gates to the mosque compound were shut by Israeli police, who cited safety concerns for 30,000 Jews praying at the Western Wall for Succot.

Jerusalem’s police chief, Aharon Franco, also incensed Palestinians on Monday by castigating them for being “ungrateful” after Israel had allowed them to pray at Al Aqsa during Ramadan. In fact, only a small proportion of Palestinians can reach the mosque. Palestinians in the West Bank and Gaza cannot get past Israel’s separation wall, and the 1.5 million Palestinians in Israel and Jerusalem are finding it harder to pray there.

Yesterday, police allowed women and Palestinian men with Israeli identification showing they were over the age of 50 to enter.

In the absence of Muslim worshippers, both the Palestinian Authority and Jordan issued statements this week warning that Jewish groups, some of whom want to blow up the mosques, should be prevented from entering the Haram. It is in this context that the leader of the Islamic Movement inside Israel, Sheikh Raed Salah, called on Israel’s Palestinian citizens to “shield the [Al Aqsa] mosque with their bodies”.

Palestinian concerns are not without foundation. Israel’s religious and secular leaders have been staking an ever-stronger claim to sovereignty over the compound since the occupation began, despite an original agreement to leave control with Islamic authorities.

The rabbinical consensus since the Middle Ages had been that Jews are forbidden from entering the compound for fear of desecrating the site of the temple’s inner sanctum, whose location is unknown.

But even as the Israeli army captured the Old City in 1967, its chief rabbi, Shlomo Goren, rushed to the Haram to read from the Bible and blow a ram’s horn, as the ancient temple priests had once done.

With official backing, Jewish settlers have been confiscating and buying Palestinian homes in and around the Old City’s Muslim Quarter, including next to the mosques.

They have also been assisted by Israeli archeologists in digging extensively under the quarter. Tensions over the excavations escalated dramatically in 1996 when Benjamin Netanyahu, prime minister then as now, approved the opening of the Western Wall tunnels under the mosques. In the ensuing violence, 70 Palestinians were killed.

In 2000, Ehud Barak, the Israeli prime minister at the time, raised Palestinian apprehensions further at the Camp David talks by demanding – against all Jewish teachings – that the compound be declared the “Holy of Holies”, a status reserved for the temple’s inner sanctum. Islamic sovereignty was challenged again in 2003 when Israeli police opened the compound to non-Muslims. In practice, this has given messianic cults, who want the mosques destroyed to make way for a third temple, access under police protection.

It was precisely rumours that Jewish extremists had entered the compound on Judaism’s holiest day, Yom Kippur, that provided the spark triggering the latest round of clashes.

A growing number of settler rabbis want the injunction against Jews praying there lifted, adding to Palestinian fears that Israeli officials, rabbis, settlers and fundamentalists are conspiring to engineer a final takeover of the Haram al Sharif.