Iraq is suffering a protracted surge in violence that has claimed more than 2,550 lives this year.
The heightened unrest has been driven mainly by widespread anger among the Sunni Arab minority, who say they are mistreated by the Shiite-led government and security forces.
It has also been fuelled by the civil war in neighbouring Syria.
Lieutenant General Hassan Karim Khudayr was killed when his helicopter experienced a "technical defect" during landing north of Baghdad, the defence ministry said in an emailed statement, without specifying when the incident occurred.
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Today, shelling in the city of Fallujah, a short drive from Baghdad, killed five people and wounded 16, while mortar rounds and twin suicide bombings in Anbar provincial capital Ramadi, farther west, left one dead and eight wounded, a doctor and a police officer said.
In a sign of both the reach of militant groups and the weakness of Iraqi security forces, all of Fallujah and shifting parts of Ramadi have been held by anti-government fighters since early January.
His body was found with eyes blindfolded and hands bound.
Violence in Iraq has killed more than 350 people since the beginning of the month, according to AFP figures based on security and medical sources.