Joe Lieberman, the Connecticut senator who is travelling with McCain, whispered in his ear and McCain quickly corrected himself.
"I'm sorry; the Iranians are training the extremists, not al-Qaeda. Not al-Qaeda. I'm sorry," McCain said.
The Arizona senator visited Iraq and Israel, as well as Jordan, during his visit to the region which was officially made on Congressional business.
Candidate judgement
The Democrats were quick to jump on the mistake by McCain, a strong supporter of the 2003 invasion and last year's troop build-up in Iraq.
"After eight years of the Bush administration's incompetence in Iraq, McCain's comments don't give the American people a reason to believe that he can be trusted to offer a clear way forward," Karen Finney, Democratic national committee communications director, said.
Brian Rogers, McCain's spokesman, said that the Republican candidate "mis-spoke and immediately corrected himself".
"Democrats have launched political attacks today because they know the American people have deep concerns about their candidates' judgment and readiness to lead as commander-in-chief," he said.
After a visit Iraq on Monday, McCain said it would be a "mistake" to pull troops out of Iraq too quickly.
"The victors in that would be the extremists, and America would lose its credibility," he said. "Al-Qaeda and the Iranian extremists would be the winners."