US military and administration officials have played down the tensions, seemingly determined not to let them interfere with plans to accelerate the transition of security responsibilities to Iraqi security forces.
But Prime Minister Nuri Al-Maliki, whose reluctance to act against Shiite militias has been a source of frustration for some US commanders, this week levelled his most direct challenge yet to US military authority: shutting down a US-Iraqi security cordon in a Shiite sector of Baghdad.
Acting as commander-in-chief of the armed forces, Maliki publicly gave US and Iraqi troops until the end of the day Tuesday to lift the cordon, which they did.
Maliki's action was especially charged because the cordon had been imposed as part of a search for a US soldier of Iraqi descent who had been kidnapped days earlier, possibly by a Shiite militia.
US officials insisted after the fact that General George Casey, the US commander in Iraq, and Ambassador Zalmay Khalilzad had agreed to lift the cordon because it was causing traffic jams and hindering commutes to work.
But the incident was only the latest in a series in which Maliki, a Shiite, has appeared to impede US military operations targeting Shiite militias, a main source of Iraq's sectarian violence.
David Gompert, a former senior defence and national security adviser to the Coalition Provisional Authority in Iraq, said there has always been an inherent tension between Iraqi sovereignty and US control over military operations.
"It's been a big issue all along of a political and legal character. It is only now that it has busted through the surface with real effects -- real political effects if not security effects," Gompert told AFP.
He said those tensions have been managed fairly well until now, but two things have changed.
"One, the American military has shown greater inclination to go after Shia militia, particularly the Mahdi army and Moqtada al Sadr," he said.
"And in parallel you now have a government that has an interest, an equity if you will, in at least the political movement represented by Moqtada al Sadr and supported by his militia."
"So now you have not just this sort of theoretical tension between the military action that is controlled by the United States and the sovereignty of the Iraqi government, but it has become very real," he said.
Michael O'Hanlon, an expert at the Brookings Institution, said Maliki's actions come at a decisive moment in US relations with Iraq.
"I think there is a decent chance that al-Maliki has basically resigned himself to the probability of civil war and he's going to make sure the Shia don't lose that war."
But O'Hanlon said the United States has little choice but to roll with the punches and look for other ways to influence the prime minister.
"I think there's a very good chance that Maliki is coming from a different place than we are, but I don't think we should give up yet," he said.
Administration and military officials have taken a conciliatory line with Maliki, stoically refusing to criticise his actions.
At the same time they have agreed to his demands for an accelerated transition to Iraqi control over its security forces.
The same day that Maliki ordered the security cordon lifted, US Defense Secretary Donald Rumsfeld announced that he had endorsed a plan to accelerate the transition and increase the size of the Iraqi security forces by another 30,000 troops beyond the current goal of 325,000.
Pentagon officials have refused to say how much the expansion will cost, how it will be equipped or how much it will accelerate the handover of control.
But nearly 18,800 of the new troops -- some 20 battalions and a special operations units -- will give the prime minister the ability to move forces to trouble spots around the country.
"More and more, the coalition forces are turning over more things to the government of Iraq than ever before," Major General William Caldwell, the military spokesman in Baghdad, told reporters this week.
"And when you start going through a period of transition, as we are in, there are going to be times when miscommunication occurs; people don't quite understand what somebody thought the other one was going to do.
"When do the authorities pass? When does the command pass? When does the control pass?"

Copyright AFP (Agence France-Presse), 2006