The Obama administration is growing worried about new sectarian bloodshed in Iraq once the military takes back territory from the Islamic State in Iraq and Syria (ISIS).

Officials in the Shiite-majority government aligned with Iran are making moves to consolidate power, quietly purging Sunnis from the rolls of the military.

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Several hundred senior Sunni officials in the Iraqi military have been fired and replaced with members of the Badr Corps, a Shiite militia created and supported by Iran, according to a U.S. official and sources in the region.

The Iraqi Ministry of Interior has also fired several thousands of other Sunni security forces in the past several weeks while continuing to arrest and “disappear” thousands of Sunnis, the sources said.

The Sunni purge is creating a new foreign policy problem for the Obama administration as it seeks to ramp up the fight against ISIS in the aftermath of the Paris terrorist attacks.

While defeating ISIS is the administration’s top foreign policy goal, pushing back the group could unleash the same sectarian warfare that erupted after the U.S. invasion in 2003.

"This isn't rocket science. We literally went through the same problem with the same people 10 years ago," said a U.S. official who recently visited the region.

One of the biggest challenges for the administration in Iraq is the growing influence of neighboring Iran.

Experts say Iran wants to maintain a land bridge from Iran to Lebanon that runs through Iraq and Syria, and that gaining control of Sunni areas such as Diyala Province is part of the plan.

To accomplish that, the Iraqi government could allow Iran-backed Shiite militias to annex parts of the country that have historically been controlled by Sunnis.

Such a move would fly in the face of President Obama’s push for a lasting peace in Iraq through the creation of an inclusive government.

The focus on the new Sunni-Shiite tensions is being amplified by the looming military effort to take back Ramadi, an ISIS stronghold in the Sunni heartland of Anbar Province.

“Ramadi will probably fall soon. The Iraqi Security Forces are a shell of their former selves. The most lethal fighting force on the ground outside of the Kurdish areas of Iraq are the [Shiite] militia controlled by Iran — that’s not healthy for us,” Sen. Lindsey Graham Lindsey Olin GrahamSenate GOP aims to confirm Trump court pick by Oct. 29: report The Hill's Campaign Report: GOP set to ask SCOTUS to limit mail-in voting Senate GOP sees early Supreme Court vote as political booster shot MORE (R-S.C.), a presidential candidate, said after returning from Iraq last week.

One influential leader from Fallujah, Iraq, said Sunnis are as fearful of the country’s Shiite government as they are of the ISIS militants who now control their towns.

“Sunnis now believe they are being held prisoners in two regions ... territories controlled by ISIS [and] jail under the rule of the Shia militias ... and they're suffering from killings and murders and rapes," said Sheikh Khamis Khanjar, a Sunni.

“The Shiite militia are just as brutal and violent as Daesh,” he added, using a different name for ISIS.

U.S. officials are also disturbed by the influence Iran and their Shiite militia proxies are wielding in the ISIS fight, seeing it as a risk to American troops.

“The Badr Corps is an unequivocally anti-American organization that’s threatening to kill American soldiers if they deploy to Iraq to fight ISIS,” said Michael Knights, an Iraq analyst with The Washington Institute and a U.S. military adviser.

The Iran-backed militias have set up checkpoints around at least one Iraqi base in Anbar Province where American forces are stationed, to control access to the base and identify who's going in and out, according to officials and experts.

"If [the U.S. does] anything that is not consistent with Iran's goals, the potential is there for an attack," said a second U.S. official.

Some officials also worry that the U.S. military is essentially acting as Iran's air force by pushing out ISIS — something a senior administration official last year vowed would not happen.

The first U.S. official told The Hill there's “absolutely” concern over the activities of the Shiite militias in Iraq.

“That's an enormous strategic problem,” the official said.

Knights said ISIS is a “flash in the pan” that will be destroyed, and the major players in the region are preparing for that outcome.

“Everyone is using this war to get what they really want,” Knights said.

The U.S. sees recruiting Sunnis into the security forces as a bulwark against Iran’s influence and are working to sign up as many as possible, especially to hold and police Sunni areas after ISIS is pushed out.

But although Sunni forces are "falling over themselves" to sign up, Baghdad has restricted their recruitment, U.S. officials and Sunni sheiks told The Hill.

An Iraqi bill to create a National Guard that would allow Sunni forces to provide security for their own areas is “effectively dead” due to Shiite resistance, according to the Institute for the Study of War’s Patrick Martin.

“The counterbalance that we need is a stronger Iraqi Army, and how do you rebuild the Army? A larger western presence, so more American troops expedites the generation of Iraqi forces that can neutralize the [Shiite] militia,” Graham told The Hill.

Obama administration officials agree more Sunnis are needed, with Defense Secretary Ash Carter telling the House Armed Services Committee last week that the U.S. continues to “urge Baghdad to enroll, train, arm and pay Sunni Arab fighters as well as Sunni Arab police forces to hold territory recaptured from [ISIS].”

But lawmakers are skeptical that will ever happen.

“I'm not getting a clear picture here other than what we've heard, over and over and over again, which is, we hope that at some point the Baghdad government actually stops persecuting Sunnis and starts including them,” Rep. Adam Smith David (Adam) Adam SmithWhen 'Buy American' and common sense collide Overnight Defense: Marine Corps brushes off criticism of Marines' appearance in GOP convention video | US troops injured in collision with Russian vehicle in Syria | Dems ask for probe of Vindman retaliation allegations Democrats press Pentagon watchdog to probe allegations of retaliation against Vindman brothers MORE (D-Wash.), the committee’s top Democrat, told Carter.

Asked by The Hill about recent actions against Sunni tribal forces, the Iraqi ambassador to the U.S. insisted that Iraqi Prime Minister Haider al Abadi has provided them with enough weapons, and said resources are tight even for the government.

But Ambassador Lukman Faily also cast doubt on the trustworthiness of the Sunni forces.

"We also need to know, who do we give the weapons to?” he said at a discussion hosted by The Diplomat. "How do you know who is a harsh jihadist?"

Senate Armed Services Committee Chairman John McCain John Sidney McCainThe Memo: Trump's strengths complicate election picture Mark Kelly: Arizona Senate race winner should be sworn in 'promptly' Cindy McCain: Trump allegedly calling war dead 'losers' was 'pretty much' last straw before Biden endorsement MORE (R-Ariz.), who visited Iraq Graham, said he’s not sure what can be done to bring Iraq together.

"The fact is that the Iranians have an overriding influence in Iraq today," he said at a Christian Science Monitor breakfast. "I saw the heavy hand of Iran in the meetings that we had with various leaders, including Abadi. ... I'm not exactly sure how to counter it.”