Many newly-trained Iraqi police and army personnel refused to fight Shia and Sunni rebels in the recent unrest, the head of US Central Command says.
Doubts hang over how Iraqis will take charge of security this year
Gen John Abizaid said this was a "great disappointment" - and announced the coalition would draw top officers from the disbanded army of Saddam Hussein.
The creation of a new Iraqi army that can follow orders is seen as key to America's withdrawal plans from Iraq.
The US had barred officers from Saddam Hussein's era serving in the military.
The reversal of policy follows a week of violence in Iraq, in which US forces faced armed opponents in Sunni-dominated zones, as well as in some formerly friendly Shia-majority cities.
Gen Abizaid said a number of Iraqi police and civil defence corps staff "did not stand up to the intimidators" during the unrest.
The US began its offensive in Falluja last Monday
His comments follow reports that a newly-trained battalion of the Iraqi army refused to support US forces as they besieged Sunni insurgents in the flashpoint city of Falluja.
It was also reported that some members of Baghdad's new police force turned against US soldiers during last week's clashes in the Shia neighbourhood of Sadr city.
"Clearly we know that some of the police did not stay with their posts and that in some cases, because we've seen films of policemen with Sadr's militia in particular, that there were some defections," Gen Abizaid said.
He said their numbers were not large but they were "troubling" to the coalition.
But he qualified his criticism by saying the US was largely "proud" of the way many of the new recruits had fought.
The US has trained at least 200,000 Iraqis to serve as police officers, soldiers and border guards in the last year.
Gen Abizaid said some problems would remain until more Iraqis occupied command positions in the new army and police.
A number of top brass from Iraq's Baathist former regime would shortly be appointed to "key positions in the ministry of defence and the Iraqi joint staff and in Iraqi field commands", the top officer announced.
"It's also very clear we've got to get more senior Iraqis involved - former military types involved in the security forces."