Held under house arrest by Saddam for a decade, could this cleric be a secret weapon for the Allies?

Iraq's most senior religious leader issued a fatwa yesterday urging the country's majority Shia community not to hinder the US and British armies. It could prove as significant a development for the invading forces as any of the military victories of the past few days.

The ruling, from Grand Ayatollah Sayyid Ali al-Sistani – the foremost Shia authority in Iraq – called on Muslims to keep calm, stay at home, not put themselves in danger and not to fight. It could add the decisive weight to the scales of war.

Certainly the fatwa provoked great optimism among the coalition's political and military leaders. Brigadier General Vincent Brooks, of Allied Central Command in Qatar, said: "We believe this is a very significant turning point and another indicator that the Iraqi regime is approaching its end."

The Ayatollah, who is 73, has been under house imprisonment at his home in the holy city of Najaf by Saddam Hussein's secret police for almost a decade. He was freed two days ago when his guards fled as US forces advanced on the city.

His decree coincided with conciliatory noises from the reformist Prime Minister of Iran – a predominantly Shia state – who voiced sorrow yesterday for the deaths of American and British soldiers.

Muslim commentators said the fatwa "could be decisive" in the outcome of the war.

US troops received a relatively warm reception from the 560,000 largely Shia locals after entering the holy city, which is the site of the tomb of Imam Ali, the son-in-law of Mohammed, whom Shias believe was the Prophet's true successor. (Islam split not long after the Prophet's death, in a manner not unlike the Catholic- Protestant schism in Christianity; Sunnis are in the majority worldwide, but Shias dominate in Iraq and Iran.)

The tomb, in the central mosque, is revered and has immense political importance. The Americans have failed to realise this in the past. In 1998 a US air strike killed 17 civilians in Najaf, handing President Saddam's Baath regime a valuable propaganda tool.

President Saddam tried to repeat the trick this time. He stationed troops inside the Imam Ali mosque, from where they fired on the Americans, hoping that US commanders would shell the shrine, in a bid to turn the Iraqi Shias and others around the world against the US.

This time, the Americans were wise to the ploy. A precision bomb took out the Baath party headquarters, which had been built near by. But US soldiers were told not to return fire at the men in the mosque.

"We've hit them very hard the last two days, wherever they're firing at us, from homes, from schools," said the American commander, Colonel Ben Hodges. "But the one place I've absolutely told them they cannot fire is into the mosque."

When the crowds of irate civilians and clerics pressed down upon US troops heading towards the grand mosque yesterday, their commanders told the soldiers to back off. The situation was defused when the soldiers – their weapons pointing down – pulled back and reassured the clerics that they would stay away from holy sites.

The ruse also backfired in the Muslim world. A Shia expatriate group in Tehran, the Supreme Council for Islamic Revolution in Iraq, condemned the Baath regime for putting soldiers into the mosque complex.

One of the first things the US military did on entering Najaf was to seek a meeting with Ayatollah Sistani. At first, the cleric refused to talk to the commanders. But then he promised he would respond to their request in two days. Yesterday he issued the fatwa.

Between 60 and 65 per cent of Iraqis are Shias. Under President Saddam they have been an oppressed majority. President Saddam is a Sunni, as are most of the dominant individuals and groups (such as the Republican Guard) in his regime.

There were tensions between the two groups during the Iran-Iraq war, though the loyalties of Iraqi Shias were complicated by feelings of nationalism. (The Iraqis are Arab, the Iranians Farsi). But during the 1991 Gulf War the Shias rose up against President Saddam, with the encouragement of the US government, who then abandoned the rebels. President Saddam harshly repressed the uprisings, killing thousands of ordinary Shias.

In the years since, the Baathist regime has murdered at least four important ayatollahs in Najaf and imprisoned six others. Besides keeping Ayatollah Sistani under house arrest, President Saddam has forced other religious leaders to issue fatwas supportive of his actions. On several occasions the Baath party issued false fatwas in the names of ayatollahs.

In September, Ayatollah Sistani issued a ruling calling on Iraqi Shias to fight against the Americans. It read: "It is the Muslims' duty, under this critical situation, to be united and do their best to defend Iraq and protect it from the plots of the aggressors."

But that was the first time his important theological school had issued such a fatwa and many opposition groups said at the time that the fatwa had been issued by President Saddam's officials. Yet so significant was the decree deemed to be that until a week ago copies of it were still pinned to the door of a main Shia mosque in Baghdad.

Yesterday's fatwa urging his flock to co-operate with the Americans is the first he has issued since being freed. Some Muslim groups immediately voiced suspicions that the Grand Ayatollah had been coerced by the US military. But it seems likely that most will accept it as legitimate, regarding the September fatwa as the one that was issued under pressure. "Of course, he was forced to do it," scoffed Abdul Majid al-Khoei, the son of the late Grand Ayatollah Abul-Qasim al-Khoei, who was Ayatollah Sistani's teacher.

Other Muslims argue that both fatwas could be lawful. "Fatwas are always circumstantial," said one prominent Islamic leader. "Judgements can change with changed circumstances, where that is for the public good. So even if the first was uncoerced, the second is binding for the new situation. It could be just what the Allies have been looking for."

There was some comfort from Iran too. Yesterday, President Mohammad Khatami had some unusually warm words for the Allies. He gave a speech on the war that was televised by the state-run station in Tehran. In it, predictably enough, he condemned the US-led invasion and said: "With this war you are giving a green light to extremist movements and violence-seekers to answer back your violence with violence". But, for the leader of a state which is traditionally hostile to America, he was also remarkably sympathetic to the Allied troops.

After voicing pity for the Iraqi people, he said: "We also feel sorry for the killed young American and British soldiers who came from another part of the world to war because of the wrong policies and motives of those who seek power."

The speech and the fatwa suggested that a tide was starting to turn. "Until now the Shias of Iraq and the followers of Sistani were confused on whether to take up arms against the Americans, whether to fight," said a spokesman for the Al-Khoei foundation, which represents followers of the Ayatollah. "This is reassuring to everyone. The regime wanted to portray the Shias of Iraq and Sistani as supporting him [President Saddam]."

In Najaf the Ayatollah also issued a Thought for the Week. It read: "At the extremity of hardship comes relief and, at the tightening of the chains of tribulation, comes ease."