The ministry pointed out the man died west of Baghdad on Monday. Hungarian media said he was 27-years-old and had been working for civilian contractors in Iraq.
"US sources informed the ministry that the car driven by Peter Varga-Balazs approached a checkpoint at high speed... he failed to slow down despite calls to stop and warning shots," the ministry said in a statement on Friday.
"Therefore, US troops fired shots at him, causing his death."
As well as civilian workers, Hungary has around 300 transport troops in the country. The shooting of Varga-Balazs was the first Hungarian death in postwar Iraq.
Also on Friday, a US soldier died of wounds sustained in a roadside bombing in northern Baghdad, said a military spokesman.
"A Fourth Infantry Division soldier was injured by an IED (improvised explosive device) in northern Baghdad yesterday (Thursday) and later died of his wounds," the spokesman told the media.