Mouwaffaq al-Rubaie also accused the UN of shying away from its responsibility towards the Iraqi people.
He also expressed his sadness at being unable to prevent the invasion in 2003.
Mr Annan told the BBC's Lyse Doucet that the current situation in
"The society needs security and a secure environment for it to get on. Without security, not much can be done - not recovery or reconstruction."
Mr Rubaie rejected Mr Annan's comments, asking: "Doesn't Kofi Annan differentiate between the mass killing of Iraqis by the security and intelligence apparatus of Saddam Hussein and the present indiscriminate killings of civilians, Iraqi civilians, by the al-Qaeda terrorists in
He added: "I'm shocked and stunned by what Kofi Annan alluded to, that the condition was better under the dictatorship of Saddam Hussein."
"We have a very worrisome situation in the broader Middle East," Mr Annan said, linking the ongoing conflicts in
He admitted that the failure to prevent the US-led invasion of
"It's healing but we are not there yet, it hasn't healed yet, and we feel the tension still in this organisation as a result of that."
Referring to the invasion, Mr Rubaie said: "The UN, I believe, shied away from the responsibilities towards the Iraqi people in 2003." Full report..
Iraq in civil war