Moments after the blasts, organisers of the conference on Sunday screamed at participants to get away from the windows of the convention centre.
The Health Ministry said 17 were also wounded when one mortar fell in the Allawi district near Haifa Street, one of the areas included in a government curfew imposed as a security measure because of the conference.
A US soldier at the scene confirmed that "a few rounds of mortars" were fired on Haifa Street, where clashes had also broken out between US soldiers and insurgents in the street. "The firing is sporadic but quite regular," he said.
Just one hour earlier, more than 100 of the delegates attending the conference stormed out - within minutes of it starting.
As soon as the UN special envoy to Iraq, Ashraf Qazi, finished his opening speech on Sunday - a large group disrupted proceedings by shouting "as long as there are airstrikes and shelling, we cannot have a conference".
Yahya Musawi, a representative of a group known as the Shia House, which worked to defuse resistance by Shia leader Muqtada al-Sadr, jumped on to the podium to address the 1300 delegates.
"Part of democracy is that you listen to the Iraqi people. It is time that you heard us and we ask that military operations stop in Najaf immediately and dialogue takes place," he shouted.
Mortars injured at least 17
people in the Green Zone
"Listen to us, prime minister, listen to us," said the protesters, as the president of the preparatory committee, Fuad Maasum, announced that there would be a 30-minute break in the proceedings.
State of war
The conference, billed as an experiment in democracy, began as at least five explosions rang out across Baghdad.
Meanwhile, tank fire and bombing resumed in Najaf - with fighting concentrated around the vast cemetery held by the al-Mahdi army and the sacred Imam Ali shrine area.
Earlier on Sunday, the local police chief ordered journalists to leave the city. General Ghalib al-Jazairi said: "I received orders from the interior minister who demands that all local, Arab and foreign journalists leave the hotel and city within two hours."
An al-Sadr spokesman said US soldiers were taking up positions around the cemetery and at the entrance to the old city in preparation for a major attack.
"We are waiting for the fighting to resume and we are ready for that," said Ali Sumaysim, blaming the failure of a truce after more than a week of heavy fighting on Prime Minister Iyad Allawi.
The premier telephoned national security adviser Muwafaq al-Rubaai just minutes before he was to sign a peace agreement that al-Sadr had already signed, Sumaysim said.
"Part of democracy is that you listen to the Iraqi people. It is time that you heard us and we ask that military operations stop in Najaf immediately and dialogue takes place"
Shia House party representative
"Rubai would have signed the agreement because we agreed on all the points ... but unfortunately Rubai suddenly had a phone call from Allawi that ordered him to withdraw and finish everything," Sumaysim said.
Al-Sadr has insisted that the US-led forces withdraw and responsibility for Najaf be handed over to the Shia religious leadership.
"The Iraqi government will be responsible for the coming massacre in Najaf. Tanks and convoys are preparing to attack the city in the coming hours," said another al-Sadr spokesman, Shaikh Qais al-Khazali, on Saturday.
Further south, a 29-year-old Dutch soldier was killed and five wounded in clashes between multinational forces and fighters, the Dutch Defence Ministry said.
It said a Dutch army vehicle near al-Rumaythah close to the Dutch base in Samawa had come under attack.
This is the second time a Dutch soldier has died in Iraq. The Netherlands has about 1300 troops stationed in southern Iraq under British command.
Elsewhere, an Iraqi group threatened to "punish" an Iranian diplomat missing since 4 August unless Iran releases - within 48 hours - 500 prisoners said to be held since its 1980-1988 war with Iraq, state television said.
Iran's al-Alam said the threat came from the Islamic Army in Iraq, which claimed a week ago to be holding Fereydun Jahani, but had made no demands.
The group, which had accused Iran of interfering in Iraqi affairs, is believed to have executed two Pakistanis already for "collaboration" with the US-led occupation forces in Iraq.