The 63-year-old suspect, identified as Hans-Josef H., will go on trial at the Koblenz court in southwestern Germany for "violating foreign trade law," the office said in a statement.
The suspect is accused of delivering the material between June 2005 and June 2007 through Turkey by hiding the nature of the shipment's contents from customs to avoid export restrictions on the material.
The businessman, who has been in provisional detention since June, is also accused of attempting to deliver another 10 tonnes of graphite to an Iranian firm that is included on a list of companies under international embargo.
The 10-tonne shipment was intercepted by Turkish customs in 2007.
Germany is part of a European diplomatic push to convince Iran to freeze its controversial nuclear programme, which Western powers fear could be used to build an atomic bomb.
Iran set alarm bells ringing in the West on Monday with its launch of a domestically manufactured satellite. The West fears Tehran could use similar technology to carry nuclear warheads.