Wasendorf "overstated the value of PFG's customer segregated funds by at least tens of millions of dollars" to the Commodity Futures Exchange Commission, according to the indictment, filed in federal court in Cedar Rapids, Iowa.
The indictment carries a possible maximum sentence of 155 years in prison, a $7.75 million fine, and 93 years of supervised release following any imprisonment, the U.S. Attorney's office said.
The public defender representing Wasendorf could not immediately be reached for comment.
Peregrine, which operated as PFGBest, filed for bankruptcy protection on July 10, one day after Wasendorf attempted suicide and left a note describing how he had bilked customers of more than $100 million over nearly 20 years.
Using little more than a post office box, laser printers and Photoshop software, Wasendorf allegedly said he forged and intercepted financial statements that were mailed between U.S. Bank, where some Peregrine customer money was held, and the firm's auditors at the National Futures Association. He said he spent most of the stolen money to try to keep his brokerage afloat.
The indictment does not mention Wasendorf's alleged misuse of customer money, but only asserts that he misrepresented the value of customer funds from February 2010 to June 2012.
An indictment means a person has been formally charged by a grand jury. Additional charges can be added later, in superseding indictments, as the grand jury continues to weigh testimony and evidence.
The federal probe into Wasendorf continues and the grand jury hears testimony from witnesses, including Russ Wasendorf Jr., son of the CEO and the company's president.
"He testified and answered all questions and continues to cooperate with the FBI," said Nicholas Iavarone, Wasendorf Jr.'s attorney.
Wasendorf is being held in a county jail and his next appearance for an arraignment has not yet been set, the U.S. Attorney's office said.