Van Anraat had originally been convicted in 2005 of complicity in war crimes for supplying Saddam Hussein, the former Iraqi president, with the raw material he used to make posioned gas in Iraq's 1980-1988 war with Iran.
The poison gas was also used against Iraq's minority Kurdish population, including an attack on the town of Halabja in 1988 which killed an estimated 5,000 people.
In the appeals trial, prosecutors tried to raise charges of genocide against van Anraat for the second time.
The businessman was acquitted of genocide charges in 2005, and the court acquitted him again, because it could not be proven he knew exactly how the chemicals would be used, a spokeswoman said.
Last December an Iraqi prosecutor at Saddam's trial showed the court an internal memo from the president's office which praised van Anraat for supplying Iraq "with rare and banned chemical weapons".
In a magazine interview in 2003, van Anraat admitted to supplying the chemicals but denied knowing they were destined for Iraq and that they would be used to make poison gas.
Prosecutors have said he shipped chemicals from the US to Belgium and from Belgium to Iraq via Jordan.
He is also said to have shipped chemicals from Japan to Italy, and then overland to Iraq.