[14] During the Iraq war, Khanfar reported from Kurdish-controlled territory in the north,[16] and after the fall of Saddam Hussein's Ba'ath regime, he became Al Jazeera bureau chief in Baghdad.

[19] This public criticism came amid attacks on Al Jazeera from US forces, including the shelling of a hotel in Basra on 8 April 2003 used solely by the channel's correspondents.

In July, Khanfar wrote an open letter to Paul Bremer, the US proconsul in Iraq responding to his assertion that television stations or newspapers guilty of "incitement to violence" would be shut down.

[19] Khanfar wrote that his offices and staff had been subject to "strafing by gunfire, death threats, confiscation of news material, and multiple detentions and arrests, all carried out by US soldiers", asserting that the channel's coverage had been consistently harassed for unfavourable reporting during the Ba'athist regime.

[19] He also said that because Al Jazeera at that time was only available in Arabic, reliance on the channel's coverage came "from second-, third- and fourth-hand sources – half-truths and total falsehoods that make the rounds in Washington, Baghdad and elsewhere.

[citation needed] In September 2011, the non-profit whistleblowing website WikiLeaks released a cache of leaked diplomatic cables highlighting U.S. activities overseas.

[26] Responding to these accusations in a 2007 interview with The Nation, Khanfar said: "Islam is more of a factor now in the influential political and social spheres of the Arab world, and the network’s coverage reflects that.

"[26] During the Iraq War, Al Jazeera broadcast a report that American troops had raided Najaf and detained the religious leaders of the Shia Islamic community, which turned out to be false.

As Saliyah Army Base, the largest pre-positioning facility of U.S. equipment in the world, served as the forward command center for CENTCOM personnel during Operation Iraqi Freedom, and Israel trade office in Qatar.

[30] In July 2009, Khanfar was invited to the United States by leading political and media think tanks including the Middle East Institute, New America Foundation, Council on Foreign Relations, and George Washington University.