Awakening Councils have helped improve security
The US defence department says the fundamental character of the conflict in Iraq remains unchanged, despite dramatic security improvements there.
In its quarterly report to Congress, it said Iraq remained locked in a communal struggle for power and resources.
The Pentagon also expressed concern at the pace at which members of Sunni militias were being integrated into the armed forces or other government jobs.
The report identified Iran's influence as the major long-term security threat.
"Despite continued Iranian promises to the contrary, it appears clear that Iran continues to fund, train, arm, and direct SG [special groups] intent on destabilising the situation in Iraq," the report said.
The US military has increased its reliance on Iraqi troops and its allies among Sunni fighters to take the lead in security operations, which is reflected in the death tolls from the last month.
The number of Iraqi security forces killed in September rose by nearly a third to 159 compared with the same period last year, while US troop deaths for the same period fell by nearly 40% to 25, according to the Associated Press news agency.
The report comes on the day that US is beginning to transfer control of about half of the 100,000 local Sunni Muslim militiamen belonging to the so-called Awakening Councils into the Shia-led government.
"The Multinational Force in Iraq is transferring the responsibility of the [councils] to the Iraq government today," a US military spokesman in Baghdad told the AFP news agency.
The move was announced at the beginning of September. Last week a US commander said the Iraqi government would start paying their salaries in Baghdad from 10 November.
Members of Awakening Councils outside the capital would come under government control at later dates.
"The slow pace of transition is a concern," the Pentagon report said.
Correspondents say the US is worried the Sunni fighters, if they are not given legitimate employment in the government, will rejoin the anti-US insurgency.
The Awakening movement was born in 2005 in Anbar province, when Sunni tribal leaders turned against former allies in al-Qaeda and worked alongside US troops.
The US military subsequently put tens of thousands of them onto its payroll and provided them with equipment and training.
The salary bill is thought to be about $360m a year.
Their successful campaign ousted al-Qaeda from Anbar within a year, transforming the huge western province into one of the most peaceful parts of Iraq.
Awakening Councils are also found among Sunni Arab tribes in Salaheddin, Diyala, Nineveh and Tamim provinces.