Hillary Clinton, the US secretary of state, said that she was only recently told about the talks and that Iraq's government would be informed of any such meetings in the future.
"We intend to make sure the Iraqi government is fully informed of any such activities, whether they are sponsored by another party or come from any other source," she said after meeting Nouri al-Maliki, the Iraqi prime minister, in Washington on Friday.
Al-Maliki said he was "quite satisfied" with the assurance.
"I have been given a commitment that the [US] administration will not negotiate or reach agreements with those who killed American soldiers, Iraqi soldiers and Iraqi people," al-Maliki said.
In an interview with Al Jazeera last week, Ali al-Jubouri, identified as head of the Political Council of the Iraqi Resistance, said his Sunni Muslim group had held talks with US officials in March and May.
He said the two sides signed a "protocol to organise the negotiation process and a document that included US recognition of the Iraqi resistance."
Al-Jubouri said the group's other demands included a formal US apology for the 2003 invasion and the release of all Iraqi prisoners, but that the talks had since broken down.
Clinton said no US officials had been authorised to sign such a deal and declined further comment.
The State Department said the Iraqi government knew about the talks at the time.
US officials have negotiated with Sunni fighters in the past, and persuaded Sunni tribal leaders, whose followers included anti-American fighters, to turn against al-Qaeda in Iraq in 2007.