US military spokesman Lieutenant Colonel Barry Johnson said US forces had conducted a raid "recently" on an al-Qaeda cell in which suspected insurgents were killed.
"We thought he may have been among those killed but now we do not believe this was the case. We do not believe that we have killed al-Masri, but we are still doing DNA tests."
Al Masri, an Egyptian who is also known as Abu Hamza al-Muhajir, assumed the leadership of al-Qaeda in Iraq after the death of Jordanian militant Abu Musab al-Zarqawi in June.
An Iraqi government source, who did not want to be named, said al Masri and three of his aides were killed in the western Iraqi town of Haditha yesterday after US forces launched an airstrike and ground assault on a safe house.
An aide to Iraqi Prime Minister Nuri al-Maliki, said DNA tests were still being conducted on the bodies. The tests suggested one of the dead was an al-Qaeda leader but not al Masri, he told news agency Reuters.
In late June, the United States put a US$5 million (A$6.72 million) bounty on the head of al Masri.