Musa Qous was still asleep Sunday morning when the muezzin at Al Aqsa mosque, right next to Mr Qous’s home in the old city of Jerusalem, called out.

But this was no ordinary call to prayer and, at eight in the morning, came at the wrong time.

“I knew there was something wrong,” said Mr Qous, 46, who works with a Jerusalem-based social rights non-governmental organisation.

Instead, the muezzin called on Muslims to come and defend the mosque and announced that Al Aqsa was in danger.

Along with what he estimated was 500 people, Mr Qous duly answered the call, only to find the gates to the mosque near his home closed and a deployment of Israeli police and soldiers stationed nearby.

With tension mounting, some of those who had gathered began chanting slogans against Israel, climbing the houses, setting fire to tyres and throwing stones at the Israeli forces that had locked them out of the mosque. The Israelis responded by shooting in the air and firing sound grenades, but the crowd refused to back down.

The unrest continued for nearly six hours. About 30 protesters were injured and 21 were arrested, including Hatem Abdul Qader, a former Palestinian Authority minister for Jerusalem affairs, according to the Israeli police. Nine Israeli police officers were also slightly injured.

This was the second time in a month that there have been serious clashes around the Aqsa mosque, the third holiest site in Islam. The clashes, then as now, started after persistent rumours that Jewish extremists were planning to damage the site.

Although most Jews consider it forbidden to walk on what they believe to be the site of the last main biblical temple, others want to rebuild the temple on the compound. And Sunday night, a group of rabbis and right-wing politicians called on Jews in Israel to gain access to the site and “ascend the Temple Mount”.

“If Jews were to increase their presence, keep coming to the Temple Mount, and if they get thrown out, come back and file a complaint, then we would gain the momentum, and I’m not talking about a few people here. I’m talking about hundreds and thousands,” Rabbi Yaakov Meidan told the Jerusalem Post.

Palestinians worry that such ideas could gain currency and put Al Aqsa mosque at risk. There have been a number of attempts in the past to destroy the mosque, most notably in 1969, when an Australian Christian attempted to set fire to the compound. According to some Christian theology, the rebuilding of the Jewish temple is necessary to fulfil biblical prophesies of the end of days.

Israel, the Islamic waqf and Jordan, which maintains an administrative role at the site, are officially committed to protecting the mosque from similar attempts, but in Israel, access to the mosque has also become a right-wing cause. Most notably, Ariel Sharon visited the mosque in 2000 with a huge security detail in a bid to lay public claim to the site on behalf of Israel, sparking massive protests that spiralled out of control and into the second intifada. Mr Sharon went on to become Israeli prime minister; he is presently comatose in a hospital.

With another right-wing Israeli government in charge under Prime Minister Benjamin Netanyahu, extremist Jewish groups have stepped up their campaign to gain access to the site, sparking fears among Palestinians that Israel is now quietly changing its official policy on Al Aqsa.

Ahmad Tibi, a Palestinian member of the Israeli parliament, yesterday accused Israel of trying to take control of the compound. He called on Arab and Islamic countries to unite to counter “Netanyahu’s aggressive policies”.

Jordan and Egypt, the only two Arab countries with peace treaties with Israel, both expressed their “grave concerns” at the incidents in Jerusalem. Saeb Erekat, the Palestine Liberation Organisation’s chief negotiator with Israel, issued a statement condemning what he described as a “deliberate [Israeli] policy of incitement”. Khalid Meshaal, the exiled Hamas leader, yesterday said only “holy war” would decide the fate of Jerusalem. In Turkey, demonstrations were held against Israel’s actions in Jerusalem.

For Mr Qous, the issue is more political than religious, and a potentially very explosive one.

“Jews have their shrine at the Western Wall. We have the Aqsa mosque and Christians have the Church of the Holy Sepulchre. Israel talks about religious tolerance, so why don’t they show us some respect?”

The issue, he said, was really about control.

“Israel wants to deepen its control over the Old City. It doesn’t want Palestinians to establish an independent state with Jerusalem as its capital. But if Israel continues with its plans against Al Aqsa, I think there will come a time when the entire region could explode.”