The endorsement by Iraq’s president of autonomous militias conducting their own counterinsurgency measures underscores a growing divide between U.S. goals and what is happening on the ground, military experts told FOXNews.com.

According to President Jalal Talabani (search), Shiite and Kurdish militias have contributed to the liberation of the country — though officials blame militia activity in recent weeks for the murder and kidnapping of Sunnis in southern Baghdad.

Talabani on June 8 heaped praise on the Badr Organization (search), formerly the Badr Brigade, the military wing of the Shia Supreme Council for the Islamic Revolution (SCIRI), Iraq’s leading political party.

“You and your [Kurdish] brothers are the heroes of liberating Iraq,” he said, also pointing to the 100,000-strong Kurdish Peshmerga, which fought against Saddam Hussein (search) in the Iran-Iraq war, helped U.S forces in the initial 2003 invasion and provides the primary security for the Kurdistan Regional Government in Northern Iraq.

“You, my brothers, march on without paying attention to the enemies’ claims because you and the [Kurdish militia] are faithful sons of the country,” said Talabani, who is a Sunni Kurd.

The reaction to these statements from Sunni leaders — who see themselves as victims of the militias — was grim.

“We do not have problems with this party or another, we only have problems with the chasing and killing of Sunni clerics and their followers,” said Abdul-Salam al-Qubeisi, spokesman for the Association of Muslim Scholars (search).

In recent weeks, some Sunni leaders have publicly blamed the Badr milita for the murder of prominent Sunni clerics and others. No one has been officially charged, and some critics have even suggested that Sunni insurgents killed the clerics as a way to enflame sectarian violence.

Prime Minister Ibrahim al-Jaafari (search), a Shiite who hailed from the predominantly SCIRI ticket in the January elections, nonetheless said there was no place for militias in the country and they should be incorporated into the police and army. A semi-autonomous offshoot of the Badr militia, the Wolf Brigade, is now operating as special forces for the Iraqi government, but has also been accused of killing Sunni clerics.

“The key duty for the government is to control all the weapons in the country,” said Jaafari spokesman Laith Kuba. Jaafari visits with President Bush in Washington on Friday.

Historically, there are numerous examples of militias across the globe, many with checkered histories and murky ambitions. Many grew out of motivation to fill security gaps, particularly for their own ethnic and religious constituencies, in failed or unstable places, like Indonesia, Africa, Bosnia and the Middle East. But in many cases, ambitions to overthrow central governments, make them often feared, rather than purely helpful.

"There is a gray area somewhere between a local militia and an insurgency itself where the ambitions are greater," said Gordon Adams, director of security studies at George Washington University.

Militias that work in quasi-governmental operations can also become corrupt, and deadly, to the government's detractors, experts add.

The most recent and emphatic example, experts point out, are the Arab Janjaweed militias, backed by the Sudanese government to beat back rebel militias. The Janjaweed have been accused of mass killings, rapes, torture and displacement of the civilian population there.

Adams said that the use of Iraqi militias are today an "alliance of convenience" in that they can supplement regional security, but it is unknown what their ambitions might be for the future.

Plus, military experts say militias may be filling a necessary gap in security, particularly in communities consistently threatened by insurgents. They play a role while the official army struggles to train and serve independently from U.S.-led coalition forces.

But analysts said the long-term presence of militias has serious implications for U.S. and Iraqi goals for a stable central government, and to avoid civil war once foreign forces eventually leave the country.

“I’m not optimistic, I would look on this with a certain foreboding,” said Vali Nasr, national security professor at the Naval Post-Graduate School in California. “If they want a centrally-controlled state and a centrally-controlled police force this is not a good way to progress.
As far as the issue of security and civil war, it’s definitely worrisome.”

Ret. Army Col. David Hunt, a FOX News military analyst, said he believes that the United States blew its chances to avoid the militia factor by its willingness to work with them in particular operations, and its failure to help the new Iraqi government disarm several militias months ago.

“We backed into this. … They got power and now you can’t take it away from them,” he said, charging that U.S. officials should draw a line — either they work more officially with the militias, or leave the areas where the militias are increasingly dominating.

“These are the types of things that three years ago we should have been thinking about and planning for,” Hunt said. “This militia issue is big because the Iraqis have got to see it as their own people helping their people. We see them as ill-trained mobs. These are two concepts that are utterly in conflict with each other.”

The Mahdi Army, the militia loyal to cleric Muqtada al-Sadr (search), fought U.S. forces for much of 2004 before agreeing to a cease-fire in October. News reports indicate that the militia is growing beyond Sadr City in Baghdad and into Shiite towns like Karbala and Basra.

U.S. officials maintain they do not support the use of unsanctioned militias, but since handing over sovereignty to the Iraqis a year ago, they don’t have much say in that anymore. When asked by reporters last week about Talabani’s recent statements, State Department spokesman Sean McCormack said “this is an Iraqi issue that they will decide and that they will deal with.”

The Pentagon declined comment for this story.

“This [Iraqi] government hangs but on a slender thread and hangs by a thread because it has such minimal loyalty and trained security capacity, and the insurgents know this,” said Adams, the George Washington University scholar, who wasn’t surprised by Talabani’s remarks.

“This smacks of internal politics to me — it’s all about how this regime can save itself,” he said. “The government is looking for whatever security forces it can get its hands on.”

Ret. Army Col. Thomas Hammes, a fellow at the National Defense University, said problems could arise in the long-term, particularly if sectarian forces begin to “cleanse” their strongholds of minorities, and begin to fight each other.

“The question is, are they just protecting their communities, or does it go beyond that?” he said. “And as Sunnis become more convinced that the militias exist only for their destruction, they are going to resist that.”

Nasr said one option is to convince the militias to fold into the national Iraqi army, a move that is being made by some members of the Peshmerga in the north, according to a recent Voice of America report.

But until stability is ensured throughout Iraq, it would be hard to diminish their role, he said.

“It’s a case,” he said, “where the reality on the ground is clearly at odds with the forces we have and the expectations we have.”

The Associated Press contributed to this report.