For many years, American diplomats have had to approach the Israeli-Palestinian conflict from a rigidly pro-Israeli position. On a personal level, that is no doubt the way they had been taught to see the world. But careerism required that they never deviate, whatever they learned on the job. The result was that, during the 1990s, all US proposals were put to the Israeli government in advance for approval.

After 23 years in the US state department, Aaron David Miller, a key figure in Middle East policy, lamented decades of missed opportunity. “For too long,” he wrote in 2005, “many American officials involved in Arab-Israeli peacemaking, myself included, have acted as Israel’s attorney, catering and co-ordinating with the Israelis at the expense of successful peace negotiations.”

It would have been more courageous, of course, if Mr Miller had spoken out before he retired. But the damage is now done. At least he confirmed what everyone had long suspected.

Mr Miller’s lament comes to mind because a revolution is brewing in the way Washington sees Israel in the context of its security commitments in the Middle East and South Asia. The rumblings of discontent come not from the state department: anyone who has dealings with US diplomats in the Arab world knows that they live in fear of mouthing a single off-message word which would have them posted to Papua New Guinea.

The change comes from the US military, in the person of Gen David Petraeus, the commander of US Central Command, whose area of operations stretches from Egypt to Pakistan.

In January a group of Gen Petraeus’s officers delivered a briefing to Admiral Michael Mullen, the chairman of the US joint chiefs of staff, which was uniquely blunt in addressing a taboo political issue. The US military posture in the region – where it is fighting two hot wars and faces an escalating confrontation with a potentially nuclear armed Iran – was eroding, the briefing said. America was viewed as weak, because it was incapable of standing up to Israel and could not make any progress towards Palestinian statehood. America was losing credibility with its Arab allies.

Nothing new here, of course, except in Washington, where Gen Petraeus – the man credited with stabilising Iraq and creating the conditions for US pullout – played the role of the boy in the fairy-tale who blurted out that the emperor has no clothes.

The logic of this briefing leaked into angry comments made by the US vice president, Joe Biden, after the Israeli government torpedoed any chance of peace talks resuming with the Palestinians by announcing 1,600 more homes for Jewish settlers in East Jerusalem.

Mr Biden is said by the Israeli press to have told Benjamin Netanyahu that Israel’s intransigence was endangering American soldiers in Iraq, Afghanistan and Pakistan.

The connection between Israeli policy and the deaths of American soldiers has now been made in Washington, and it is very damaging for Israel.

The question remains, is this a real revolution in the way the US deals with Israel? Gen Petraeus has stated in public that the Israeli-Palestinian conflict “foments anti-American sentiment due to a perception of US favouritism towards Israel”. We know that Mr Biden endorses this thinking and must suppose that President Barack Obama shares it to some extent.

The military logic is convincing. Ever since the US declared a “war on terror”, put boots on the ground in Iraq and Afghanistan, and prepared for war with Iran, it was inevitable that Washington’s search for Muslim allies in the region would clash with its long tradition of indulging Israel.

In 2006 the Iraq Survey Group report, commissioned to explore ways to get out the Iraq quagmire, concluded that Washington could no longer compartmentalise Israel-Palestine away from the rest of the Arab world.

“The US will not be able to achieve its goals in the Middle East unless the US deals directly with the Arab-Israeli conflict,” said the report, co-authored by James Baker, the former secretary of state.

The Bush administration balked at taking this advice, and proceeded with the usual milk-and-water diplomacy, known as the Annapolis process. Mr Baker’s conclusion has now been repackaged in starker terms for more desperate times.

Mr Baker has some form in this matter. It was he who bludgeoned Israel into attending the 1991 Madrid peace conference by withholding US loan guarantees. We are still far from a rerun of the 1991 wrestling match with the Israeli government. The latest comments from Washington have tried to tone down the argument with Israel. The Obama administration is clearly too weak politically for a full blown fight with Israel.

But something has changed: military thinking has come to the fore, after eight years of fighting in Afghanistan and Iraq. The military mind sets a goal, identifies the obstacles in the way and then proceeds to obliterate them. If one of these obstacles causes the deaths of US soldiers, it is all the more urgent to address it.

The craft of diplomacy, however, works differently: it uses smiles and complex forms of words to smooth over problems. If foreigners are being killed – particularly Palestinians – they can be ignored. The problem is left for another day. Gen Petraeus is pointing out that business as usual, the default mode of diplomacy, gets in the way of achieving his military goals.

It may be too early to expect a showdown with Israel, but the military has started a debate about the place of Israel in America’s national security. That, at least, is a start.