Dietary supplements, pain killers, fake contact lenses, epilepsy medication and 1.2 tonnes of erectile dysfunction pills were among the drugs seized, the agency, based in Lyon, France, said in a statement.
Operation Pangea X was carried out by police, customs and health authorities across a record 123 countries and led to more than 400 arrests from September 12 to 19.
The illegal sale of medicine online was also targeted, with 3,584 websites shut down and more than 3,000 online advertisements suspended.
"The sale of fake or counterfeit pharmaceuticals is a growing concern across Africa, as it creates a dangerous situation for the health of unsuspecting consumers," Sam said.
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As opioid abuse has reached epidemic proportions in several countries, the operation also targeted the trade of painkillers, particularly the drug Fentanyl.
Numerous websites selling only the drug were closed down, including one called "Where to buy Fentanyl without a prescription".
Operation Pangea was launched in 2008 and has since tracked the rise of unauthorised websites selling pharmaceutical products.
"The fact that we still see such strong outcomes after 10 years of Pangea operations demonstrates how the online sale of illicit medicines is an ongoing, and ever increasing, challenge," he said.
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