Some suspected insurgents held in Iraqi custody suffered abuse, according to the leaked records
The documents also suggest "hundreds" of civilians were killed at US military checkpoints after the invasion in 2003.
And the files show the US kept records of civilian deaths, despite previously denying it. The death toll was put at 109,000, of whom 66,081 were civilians.
The US criticised the largest leak of classified documents in its history.
A US Department of Defense spokesman dismissed the documents published by the whistleblowing website as raw observations by tactical units, which were only snapshots of tragic, mundane events.
On allegations of abuse, he said it was policy always to report "potentially illegal abusive behaviour" so action could be taken.
Speaking to reporters in Washington earlier, US Secretary of State Hillary Clinton said she condemned "in the most clear terms the disclosure of any information by individuals and or organisations which puts the lives of United States and its partners' service members and civilians at risk".
Wikileaks founder Julian Assange told al-Jazeera television that together with public interest lawyers in the UK, the website had "produced papers for a lawsuit for 40 wrongful killings in Iraq".
'Nothing new'
The 391,831 US army Sigacts (Significant Actions) reports published by Wikileaks on Friday describe the apparent torture of Iraqi detainees by the Iraqi authorities, sometimes using electrocution, electric drills and in some cases even executing detainees, says the BBC's Adam Brookes, who has examined some of the files.
The US military knew of the abuses, the documents suggest, but reports were sent up the chain of command marked "no further investigation", our correspondent adds.
One document shows the US military was given a video apparently showing Iraqi Army (IA) officers executing a prisoner in the northern town of Talafar.
"The footage shows the IA soldiers moving the detainee into the street, pushing him to the ground, punching him and shooting him," states the log, which also names at least one of the perpetrators.
In another case, US soldiers suspected army officers of cutting off a detainee's fingers and burning him with acid.
Pentagon spokesman Geoff Morrell told the BBC that if abuse by the Iraqi security forces was witnessed, or reports of it were received, US military personnel were instructed to inform their commanders.
"And at the appropriate level that information would then be shared with the Iraqi authorities and the military for them to take action."
The documents also reveal many previously unreported instances in which US forces killed civilians at checkpoints and during operations.
In one incident in July 2007, as many as 26 Iraqis were killed by a helicopter, about half of them civilians, according to the log.
Another record shows an Apache helicopter gunship fired on two men believed to have fired mortars at a military base in Baghdad in February 2007, even though they were attempting to surrender. The crew asked a lawyer whether they could accept the surrender, but were told they could not, "and are still valid targets". So they shot them.
The helicopter - with the callsign "Crazyhorse 18" - was also involved in another incident that July in which two journalists were killed and two children wounded.
There are also new indications of Iran's involvement in Iraq, with reports of insurgents being trained and using weapons provided by the Islamic Revolution Guards Corps (IRGC).
Finally, the documents appear to show that the US military did keep records of civilian deaths, despite earlier denials that any official statistics on the death toll were available.
The logs showed there were more than 109,000 violent deaths between 2004 and the end of 2009.
They included 66,081 civilians, 23,984 people classed as "enemy", 15,196 members of the Iraqi security forces, and 3,771 coalition troops.
Iraq Body Count, which collates civilian deaths using cross-checked media reports and other figures such as morgue records, said that based on an analysis of a sample of 860 logs, it estimated that around 15,000 previously unknown civilian deaths would be identified.
An IBC spokesperson commented: "It is totally unacceptable that for so many years the US government has withheld from the public these essential details about civilian casualties in Iraq."
The UK's Guardian newspaper also reported that the US military appeared not to have recorded any civilian deaths during its two major offensives on the city of Falluja in 2004.
Mr Morrell, of the Pentagon, told the BBC that the leak was a "travesty" which provided enemies of the West with an "extraordinary database to figure out how we operate".
He said the cache of documents contained "nothing new" with regards to fundamental policy issues.
"It may provide us with some additional detail, with some additional anecdotes, but the price we pay in doing so is that it could compromise the wellbeing of our forces," he said.
And he once again asked Wikileaks to remove the documents from the web and return them to the Department of Defense.
Wikileaks has said it has deleted all names from the documents that might result in reprisals.
US Defence Secretary Robert Gates suggested the whistle-blowing website had blood on its hands in July after it published more than 70,000 secret papers about the war in Afghanistan.
The investigation into the Afghan leak has focused on Bradley Manning, a US army intelligence analyst who is in custody and has been charged with providing Wikileaks with a video of the July 2007 attack by a helicopter with the callsign Crazyhorse 18.
The release of the documents comes as the US military prepares to withdraw all 50,000 remaining troops from Iraq by the end of 2011.
Violence in the country has declined sharply over the past two years, but near-daily bombings and shootings continue.
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