The documents, from at least three companies, contained information about military aircraft engines, the Hartford (Conn.) Courant reported Wednesday.
The engineer, Mozaffar Khazaee, 59, was arrested last month in Newark, N.J., as he prepared to fly to Tehran. He pleaded not guilty to all charges Wednesday.
Assistant U.S. Attorney Stephen Reynolds told federal Magistrate Judge William I. Garfinkel the money, totaling $59,945, was found in Khazaee's carry-on luggage.
The seizure was disclosed in an updated indictment that added a count of transporting property stolen from a third company across state lines. Federal prosecutors previously identified one of the companies as Pratt & Whitney, but have not named the other firms.
Federal authorities say Khazaee shipped thousands of sensitive and proprietary documents across the United States with the intention of having them taken by freighter to Iran.
Customs authorities in California discovered the documents in November.