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The battle over Falluja has evolved into yet another example of how United States and Iranian interests seemingly converge and clash at the same time in Iraq. Both want to defeat the Islamic State, also known as ISIS

In Syria, where the government of Bashar al-Assad is an enemy, America’s ally is the Kurds.

But in Iraq, where the United States backs the central government, and trains and advises the Iraqi Army, it has been limited by the role of Iran, the most powerful foreign power inside the country.

In an extraordinary statement on Wednesday, Grand Ayatollah Ali al-Sistani, the world’s pre-eminent Shiite religious leader, who lives in Najaf in southern Iraq and is said to be concerned by Iran’s growing role in Iraq, urged security forces and militia to restrain themselves and abide by “the standard behaviors of jihad.”

The United States has thousands of military personnel in Iraq and has trained Iraqi security forces for nearly two years, yet is largely on the sidelines in the battle to retake Falluja. It says its air and artillery strikes have killed dozens of Islamic State fighters, including the group’s Falluja commander.

Militiamen have plastered artillery shells with the name of Sheikh Nimr al-Nimr, a Shiite cleric close to Iran whose execution this year by Saudi Arabia, a Sunni power, deepened the region’s sectarian divide, before firing them at Falluja.

Prime Minister Haider al-Abadi, who has stressed that civilians must be protected in the operation and ordered that humanitarian corridors be opened to allow civilians to leave the city safely, disavowed the militia leader’s comments.

She said that some residents had been killed for refusing to fight for the jihadists, and that those inside were surviving on old stacks of rice, a few dates and water from unsafe sources such as drainage ditches.

To allay fears that the battle for Falluja will heighten sectarian tensions, Iraqi officials, including Mr. Abadi, and militia leaders have said they will adhere to a battle plan that calls for the militias not to participate in the assault on the city.

The American military role in Iraq has been limited mostly to airstrikes and the training of the army. But, as in northern Syria, there are also Special Forces soldiers in Iraq, carrying out raids on Islamic State targets.

Iraq’s elite counterterror forces are preparing to lead the assault on Falluja; they have long worked closely with the United States and are considered among the few forces loyal to the country and not to a sect.

A big question going into the battle is whether the Islamic State fighters will dig in and fight or, as they have in some other battles, throw away their weapons and try to melt into the civilian population.

For the United States, there is also the matter of history: Led by the Marines, its forces fought two bloody battles for Falluja in 2004. Mindful of this past, American officials would have preferred that the Iraqis left Falluja alone for now and focused on the Islamic State stronghold of Mosul in the north.

The American military’s assault on Falluja in April of 2004 was in retaliation for an episode that became an early symbol of a war spiraling out of control, the image of it as indelible as it was gruesome: the bodies of four Blackwater contractors dangling from the ironwork of a bridge.