"Coalition commanders have been able to engage some insurgents to explore ways to collaborate in fighting the terrorists," Khalilzad said in Baghdad at his final news conference as the US ambassador to Iraq.
He said: "These insurgents are also in touch with the government seeking reconciliation and co-operation in the fight against the al-Qaeda terrorists."
Speaking to Al Jazeera from Baghdad, Abdul-Rahman al-Qaesi, spokesman for the Jaish al-Mujahideen group, denied claims made by Khalilzad.
He said: "The US wants to veil the truth of being an occupation side. And by saying it is holding talks with those fighting it, wants to sow suspicion among armed groups about some among them having contacts with the Americans."
Khalilzad said US and Iraqi officials had met representatives of Sunni Arab groups several times for talks. He said they are continuing to take place, but declined to give specifics because "people's lives are at stake".
He said the government must demobilise militias, schedule provincial elections, amend the constitution to address Sunni concerns and reach agreement to "allow insurgents to lay down arms and join the political process".
Asked if US contacts with "insurgent" groups did not violate its policy of not talking to "terrorists", he said: "I did not say we've talked to terrorists," drawing a distinction between terrorists and "reconcilable" insurgents.
"One of the main challenges is how to separate more and more groups away from al-Qaeda.
"There's a real struggle going on in the Sunni Arab part of Iraq between al-Qaeda and the other more patriotic groups."
Meanwhile, the US army said that five US soldiers were killed in two separate attacks in the provinces of Diyala and Baghdad on Sunday.
It also said that three foreigners, including an American, were injured by mortar shells fired at the Green Zone.
In Baquba, Iraqi police said that dozens of civilians were killed and wounded after US helicopters launched an air strike on a village north of the city.