This letter is an extraordinary document. Provided that it is authentic, of course.

There is no obvious reason to doubt the Pentagon’s statement that this is a message from Ayman al-Zawahiri, Osama bin Laden’s deputy, to Abu Musab al-Zarqawi, head of al-Qaeda in Iraq.

But the 6,000-word text contains puzzles, and the timing of its release is hardly casual.

It comes only three days before Iraq holds a referendum on its constitution, and the US desperately needs Iraq to vote “yes” to plan its own exit.

The letter is not entirely helpful to the US. Parts are alarming; they show al-Zawahiri as a sophisticated political tactician.

But the text also gives the West reason to hope that it has crippled al-Qaeda — and that the group is riven by factions. It shows that al-Qaeda wants to provoke Iraqi civil war and gives Iraqis who want peace more reason to back the referendum.

The most startling passage argues that al-Qaeda should stop killing Shia civilians, and stop cutting off the heads of Western hostages. It will lose the support of ordinary Muslims, and with it, the war, the letter says.

“We are in a battle, and more than half of this battle is taking place in the battlefield of the media,” says al-Zawahiri. He asks, too, whether “the opening of another front now in addition to the front against the Americans and the Government (is) a wise decision”.

He warns fighters against “highlighting the doctrinal differences (within Islam) which the masses do not understand”. There must be doubt whether al-Zarqawi, who is thought to enjoy beheading hostages, is the best audience for this subtle doctrinal analysis.

But the letter, while threaded with reverence for Islamic doctrine, is astonishing for its political pragmatism.

The tone is confident; al- Zawahiri takes an early exit by the US as given. He states bluntly that al-Qaeda’s “intended goal is the establishment of a caliphate . . . in the heart of the Islamic world”. But he is clearly worried about controlling the fighters in Iraq, who might lose sight of their target in their feud with the Shias.

There is a central conflict in the letter which represents al-Qaeda’s greatest dilemma. The group, Sunni to its core, cannot take advantage of the US’s predicament in Iraq, because the war has produced a Shia-led Government.

Al-Zawahiri talks of the “treason of the Shia and their collusion with the Americans . . . in exchange for the Shia’s assumption of power”. He recommends “forgiving” ordinary Shias because they are “ignorant”, but says a “collision” between a Sunni state and the Shias “is a matter that will happen sooner or later”.

This is a jumbled prescription: concentrate on getting the Americans out — but then turn on the Shias.

The letter also shows that al-Qaeda in Afghanistan is severely weakened. It talks of the “real danger” of the Pakistani army, and of “difficulty and hardship”. It asks al-Zarqawi for money and pleads for details about Iraq, saying: “At the least, we should know as much as the enemy knows.”

It is also deferential to al- Zarqawi, saying several times that those afar cannot second-guess his judgment. There is a strong hint that the power in al- Qaeda has moved from the men in the mountains to their nominal juniors in Iraq.

Al-Zawahiri appears dismissive of the Afghan war, a “far-flung” battle, and “just the groundwork . . . for major battles”.

He criticises the Taleban for failing to win popular support and collapsing within days of the US assault. His presumed hosts in the Afghan-Pakistan border would hardly thank him for that. There are puzzles, it should be said. There is no reference to the London bombings, although this letter is dated two days afterwards; perhaps this is because television was inaccessible, but it is still surprising.

Al-Zarqawi, the intended recipient according to the Pentagon, is also, oddly, referred to briefly in the third person.

What effect might this letter have on Saturday’s referendum? It would make Shias more inclined to vote “yes” — but they would anyway.

The effect on Sunnis is harder to predict. Sunnis who want to overthrow the Shias might seize this text as proof that al-Qaeda is still the best game in town. But those who want peace might be more inclined to back the constitution.

The Pentagon must have reckoned there are more of the second group than the first.

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