The truck, intercepted on a motorway in northern Spain early on Wednesday, was carrying highly corrosion-resistant valves, the ministry said in a statement.
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Police were examining computer databases and documents at the company, Fluval Spain, a ministry spokesman said. The two arrested men were employees at the firm, he said.
"The company, registered in the Basque Country, used false companies in the United Arab Emirates for the deliveries, channeling cash through banks in other countries," the ministry statement said.
The company had commercial links with Iranian firms that featured on lists drawn up by the European Union as having connections with Tehran's nuclear program, the ministry said.
No-one at the company could be reached for comment.
The European Union has banned the sale of such material to Iran, which denies Western accusations it is seeking to develop a capability to make nuclear weapons. Tehran says its atomic program is for civilian energy purposes.
World powers are searching for a diplomatic solution to a decade-old standoff over the nuclear program to avert the threat of a Middle East war.