"I cannot confirm this information just now," Qassim al-Mussawi, the Iraqi defence ministry spokesman, said after the news was reported on state television.
An Iraqi defence official who asked not to be identified told the AFP news agency that the only evidence the army had that it had wounded al-Masri was a report from "soldiers who said they saw him escape".
An internet statement purportedly from the Islamic State in Iraq said: "The fabrication of such reports by the government - which was even denied by their American masters - is proof of their bankruptcy and confusion."
The authenticity of the statement could not be verified but it was posted on a website often used by Islamic groups.
Al-Masri, also known as Abu Hamza al-Muhajir, was thought to have took over the leadership of al-Qaeda in Iraq after Abu Musab al-Zarqawi was killed in a US airstrike last June.