As security forces launched a major manhunt to recapture those on the run, Iraq's interior ministry said the gunmen who attacked prisons at Abu Ghraib and Taji on Sunday night had been in "conspiracy" with guards at both facilities.
The scale of the assault has prompted warnings of "dark months ahead" as the freed inmates - some of whom were top al-Qaeda operatives - launch new campaigns against the government. A statement from the interior ministry said:
"There has been a conspiracy between some of the guards of both prisons and the terrorist gangs that attacked the prisons."
The allegation from the Iraqi government came as responsibility for the jailbreak was claimed by the Islamic State of Iraq and the Levant, an al-Qaeda franchise that many Sunni extremists in Iraq follow.
In a statement brimming with sectarian venom, it said the assault - one of the largest and most sophisticated insurgent operations ever carried out in Iraq - was the result of months of careful planning against Baghdad's Shia-dominated government.
"The mujahideen [holy warriors], after months of preparation and planning, targeted two of the largest prisons of the Safavid government," the group said. Safavid is used by hardline Sunnis as a derogatory term for Shia Muslims.
More than 50 people, including 26 guards and Iraqi soldiers, are now known to have died in the attacks, in which teams of gunmen and suicide bombers mounted synchronised assaults on both jails. Iraq's justice ministry said that 260 prisoners had been freed, and that around 150 had been caught again.
The al-Qaeda statement claimed that more than 500 had been freed, and that 120 Iraqi guards had been killed.
Questions were also asked as to why it took the Iraqi government 10 hours to send in helicopter gunships to quell the fighting at Abu Ghraib, a delay that some said suggested poor command and control within the security establishment.
One Iraqi politician, who asked not to be named, claimed that the assault on the prison at Taji was planned simply to divert security forces from what was to be the main strike at Abu Ghraib, where an estimated 15,000 inmates are held.
He added that a number of senior Sunni guards at Abu Ghraib had gone missing since, and that it was possible that they had been acting as "inside men". Other reports claimed that inmates had started riots just prior to the attacks to distract the guards, and had been armed with weapons.
"We are preparing for a very bad storm in the next few months now that these inmates have been released," the politican said. "We are talking about hard-core al-Qaeda here. Some were previously held by the Americans."
The attack came exactly a year after the leader of al-Qaeda's Iraqi branch, Abu Bakr al-Baghdadi, launched a campaign called "Breaking the Walls", aimed at freeing imprisoned comrades.
Last September al-Qaeda launched a similar operation that freed more than 100 inmates from a prison in Saddam Hussein's home town of Tikrit.
The ability of al-Qaeda to strike at the Iraqi government's most heavily-guarded facilities shows how the organisation has regrouped in the last two years - and also how the Iraqi government is struggling to maintain security.
Toby Dodge, an Iraq specialist at the London School of Economics and author of Iraq: from war to a new authoritarianism, said: "It was one hell of an operation and speaks very much to the reconstitution of al-Qaeda's capacity. It also shows a Keystone Cops element to the Iraqi government's response."
Colin Freeman is a journalist for the British based Telegraph newspaper