"Outlawed groups through terrorist attacks like explosions, assassinations, kidnappings or forced displacements created these terrible figures, which represent a huge challenge for the rule of law and for the Iraqi people."
The report did not distinguish between civilian deaths and others, and a senior government official said the findings did not include missing persons, believed to be around 10,000 people.
It said some 15,000 unidentified bodies were also found within the time period.
"Thousands of Iraqis killed since 2003 without being identified by their relatives were buried in special cemeteries called unidentified body cemeteries," the report said.
The figures in the report are lower than that of the Iraq Body Count project run by a group of academics and peace activists.
The project estimates that 102,071 civilians have died in the violence so far since 2003.
The group took its figures from media reports, which it then cross checked with numbers from hospitals, morgues and local non-governmental organisations.
But the figures from both the Iraqi government and the Iraq Body Count project are lower than the numbers from a 2006 study by The Lancet, a British-based medical journal.
The Lancet estimates 601,000 people were killed in Iraq between 2003 and 2006.
A recent spike in violence in Iraq has been blamed on Iraq's neighbouring countries, including Syria and Iran.
Baghdad has accused Syria of harbouring former Iraqi Baathists and the US has accused Iran of funding, arming and training armed groups operating in Iraq.
Hoshyar Zebari, the Iraqi foreign minister, has called on neighbouring countries to stop stoking instability in his country.
On Wednesday, Wijdan Salim, Iraq's human rights minister, said that she also believes neighbouring countries are making unrest worse in Iraq.
"They need to stop interfering and stop the terrorism from entering Iraq by their borders," Salim told Al Jazeera.
But she said she believes the security situation in Iraq will soon change for the better.
"I am very pained for anyone who lost his life. But ... we are trying to change the whole situation in Iraq, to have a democracy, to have a new government, to have the rule of law.
"We hope that 2010 will be different than now."