In a television interview on Friday, al-Jafari expressed dismay over US claims that up to 300 Mahdi Army fighters had been killed in Najaf and said it was hardly the civilised way to rebuild Iraq.
"Of course when I hear of the deaths of Iraqi civilians, I cannot find any justification for the killings," al-Jafari said.
"I think that killing Iraqi citizens is not a civilised way of building the new Iraq, which is based on protecting people and promoting dialogue, not bullets."
US marines claim they have killed 300 Mahdi Army fighters in Najaf in the past two days, but a spokesman for Shia leader Muqtada al-Sadr said most of those killed were civilians.
A spokesman for al-Sadr, Shaikh Ahmad al-Shaibani said only nine fighters were killed and 20 wounded in clashes with US-led occupation forces.
That figure was later revised to 36 killed militia fighters.
The Iraqi vice president also criticised the Najaf governor, Adnan al-Zurfi, for issuing an ultimatum to the Mahdi Army fighters to leave the city in 24 hours, branding them as criminals.
"I think decisions like this should have been taken centrally ... in Baghdad rather than locally," he said.
Al-Jafari was unable to say whether the US had sought authorisation from the interim government before launching its assault on Najaf.
"Maybe this is what happened, or maybe not," he said. "But I am not aware of the details of such an agreement".