We've read a lot about Shia militia infiltration of the Iraqi police and Interior Ministry security forces, but most reports seem to emphasize that the Iraqi Army is more professional. This report from Baghdad seems to indicate otherwise:
U.S. Army commanders and enlisted men who are patrolling east Baghdad, which is home to more than half the city's population and the front line of al-Sadr's campaign to drive rival Sunni Muslims from their homes and neighborhoods, said al-Sadr's militias had heavily infiltrated the Iraqi police and army units that they've trained and armed.

"Half of them are JAM. They'll wave at us during the day and shoot at us during the night," said 1st Lt. Dan Quinn, a platoon leader in the Army's 1st Infantry Division, using the initials of the militia's Arabic name, Jaish al Mahdi. "People (in America) think it's bad, but that we control the city. That's not the way it is. They control it, and they let us drive around. It's hostile territory."

...

Al-Sadr's gunmen got another boost in 2005 and 2006 when American commanders handed over many Baghdad neighborhoods east of the Tigris River to Iraqi units, transitions that often were accompanied by news releases that contained variations of the phrase "Iraqis in the lead."

"There's been a lot of push to transition to Iraqis so you can show progress, but have you secured the area?" said Capt. Aaron Kaufman, a Washington, Iowa, native who works for a unit that acts as a liaison between U.S. and Iraqi forces in the Shiite enclave of Kadhamiya, across the river from east Baghdad. "I think the political pressure has hurt. ... You're wishing away, you're assuming away enemy activity, and you hurt yourself doing that."

In hindsight, many American officers said there was too much pressure to give Iraqi army units their own areas of operation, a process that left Iraqi soldiers outmanned, outgunned and easy targets for infiltration and coercion.

...

Iraqi soldiers, for example, often were pushed into the field by Iraqi commanders who didn't give them adequate food, clothing or shelter, said Etienne, a 1st Infantry Division platoon leader.

Etienne was on patrol one day when he saw Iraqi soldiers eating fresh vegetables and meat. The afternoon before, the same soldiers had complained that they had only scraps of food left. Who'd brought them their meal? It had come courtesy of Muqtada al-Sadr.

"Who's feeding the Iraqi army? Nobody. So JAM will come around and give them food and water," Etienne said. "We try to capture hearts and minds, well, JAM has done that. They're further along than us."

There's been ample evidence - despite claims to the contrary by American and Iraqi officials - that the death-squad activity isn't isolated to a few troops loyal to al-Sadr.

In the southeastern Baghdad neighborhood of Zafrainyah, an entire national police brigade was sent to be retrained last year- and much of its leadership was replaced - after its officers kidnapped 24 Sunnis, took them to a meat-processing plant and killed them.

Last month, four members of a neighborhood council in Etienne's sector - a mixed Sunni-Shiite area that abuts an al-Sadr stronghold - were leaving a meeting when national police trucks pulled up and men in Iraqi military uniforms piled out.
They grabbed the four men in broad daylight. One of the council members struggled. He was shot in the head and left to die on the street.

The remaining three were blindfolded and driven to a house. One of the four, a Shiite, listened as his two Sunni colleagues begged for their lives between beatings.

"They were pistol-whipping them and kicking them," Etienne said. "Finally, he heard the sound of a drill."

When the man's blindfold was taken off, he found that he was covered with the blood of his two friends, who were slumped over dead with drill holes in their heads.

"It was (al-Sadr's militia). They were trying to figure out who's who, and killing Sunnis," Etienne said. "They borrowed the vehicles from their friends in the Iraqi army and police who are Mahdi-affiliated."

...

A soldier with a U.S. Army tactical human-intelligence team - who goes only by his last name, Brady, because of the sensitivity of his work - gathered a group of Sunni men to ask about neighborhood security.

One of the men, who said his name was Abbas al Dulaimi, asked, "When the Mahdi Army comes here, why does the Iraqi army help them shoot people?"

"I was behind a car at the checkpoint on the bridge. I saw an Iraqi army soldier open the trunk," said another man, who gave only his first name, Ahmed. "There were two men in there. The driver showed the soldier his Mahdi Army ID, and the soldier saluted him and let him drive away."

Brady didn't contradict any of the accounts. He took careful notes, shaking his head sympathetically at their stories of an Iraqi army gone astray.

He handed out a business card with a cell phone number to call in case of another Mahdi Army attack.

"We will send Iraqi army units that we trust," Brady said.

Abbas al Dulaimi stared at Brady, a blond man sitting in a circle of Iraqis, and spoke as if he were explaining something to a child.

"But if the Mahdi Army comes in here," Abbas al Dulaimi said, "they will come with the support of the Iraqi army."
Brady didn't contradict him.