At a news conference on Tuesday, Zalmay Khalilzad said the US was seeking to make contacts with some of the armed groups in Iraq.
"We are reaching out to everyone but two groups: the Zarqawi group and associated forces who are jihadists ... and the Saddamists, those who want Saddam Hussein to return," he said.
Khalilzad added that if the US wanted a properly functioning Iraq, then Sunnis must be given the opportunity to take part in the political process.
Sulayman al-Jumaili, spokesman for the Iraqi reconciliation front, told Aljazeera: "What guarantees or roadmap is the US going to offer to encourage these groups to join the political processes or direct negotiations?
"We in the Iraqi reconciliation front have put on top of our priorities the integration of genuine resistance groups into the Iraqi political process. It is imperative that such resistance should be recognised."
Khalilzad told ABC television on Tuesday that he was seeking talks with neighbouring Iran to help in the fight against resistance.
"We are not seeking hostile relations between Iraq and Iran ... I think we will be talking very frankly and encouraging Iran not to interfere with the new Iraqi affairs," he said.
US State Department spokesman Sean McCormack said any such contacts would have no consequence for relations with Iran that were broken off after US diplomats in Tehran were taken hostage in 1979.
"We are not seeking hostile relations between Iraq and Iran ... I think we will be talking very frankly and encouraging Iran not to interfere with the new Iraqi affairs"
US ambassador to Iraq
"It's a very narrow mandate that he has, and it deals specifically with issues related to Iraq," McCormack told reporters.
Khalilzad said he received permission from President Bush to begin a diplomatic dialogue with Iran to help to secure Iraq after the US troops' pullout in phases.
In an earlier interview with the Newsweek magazine, Khalilzad said: "I've been authorised by the president to engage Iranians as I engaged them in Afghanistan directly.
"There will be meetings, and that's also a departure and an adjustment," he said.
An Iranian morning daily on Tuesday urged Iranian officials to consider rationally the Khalilzad proposal to talk with Tehran.
Iran's official news agency IRNA quoted the English-language daily Iran News as saying: "Some observers believe the US has finally come to the realisation that stability in the region is not achievable without Iran."