He urged Sunni groups to participate in the reconciliation meeting.
"If you want to fix something, you can't do it by boycotts. Everybody should participate," he said.
But the National Concord Front said only certain members of its organisation had been invited to attend the meeting.
"The Concord Front will not attend the conference as we were not invited as a bloc," Salim Abdallah, a spokesman for the group, said.
He said the bloc was also protesting at the way Iraq handled the case of a former deputy minister who was acquitted on allegations of organising Shia death squads that targeted Sunnis.
Earlier the month, an Iraqi court freed Hakim al-Zamili, a former deputy health minister, saying there was no evidence against him.
Brigadier General Hamid al-Shammari, the health ministry’s security chief, was also acquitted during the same trial.
"The Zamili case has emerged as a big obstacle in reconciliation, because the way it was handled has not satisfied the Concord Front," Abdallah said.
The two-day conference in Baghdad comes as a US military commander said that progress towards lasting peace in Iraq has been too slow.
General David Petraeus, told the Washington Post that "no one" in the US and Iraqi governments "feels that there has been sufficient progress by any means in the area of national reconciliation".
In recent months the US has sent 30,000 extra troops to Iraq in what it calls an attempt to rein in sectarian violence.
Dick Cheney, US vice-president, said on Monday during an unscheduled visit to Iraq that he was wary of large-scale US troop cuts.
He said that any advances in security for Iraqis would be wiped out should troops be pulled out of the country.
The aim of the troop 'surge' is to give Iraq's leaders a chance to pass a raft of laws intended to attract armed groups back into mainstream politics, but parts of the legislation package have stalled in parliament.
The peace talks are the second attempt by Maliki to end sectarian fighting that has gripped the country since suspected Sunni fighters blew up a Shia shrine in February 2006.