The clerk, employed at Itarsi railway station in Madhya Pradesh, has been booked for cheating the government by accepting the licence fee in the form of demonetised currency notes in violation of the government's November 8 notification.
The government had declared Rs 1,000 and Rs 500 notes as illegal tender from November 8 midnight.
The CBI official said the clerk allegedly entered into a criminal conspiracy with an Itarsi-based private firm, dealing in food services with the Indian Railway, and other unknown persons.
"The clerk deposited old currency notes in cash amounting to more than Rs 61 lakh on November 9 last year as advance yearly licence fee in railway account for their units at Itarsi and Bina railway stations," the official said.
He further said that separate the CBI team also conducted searches at four places, including the residential and office premises of the clerk and the proprietor of the private firm at Itarsi district and recovered several incriminating documents.