The 50-year-old, who was led to US district court in handcuffs on Thursday, made no comment outside court, but his lawyers vigorously protested his innocence.
"Jeff Skilling has nothing to hide. He didn't steal. He didn't lie. He didn't take anyone's money," said his lawyer Dan Petrocelli.
"In the 60 pages of charges filed by the US government, they don't even accuse him of these things, and it's not for lack of trying," he continued.
"I guess they need a scapegoat, and I guess Jeff Skilling is their scapegoat."
Skilling has steadfastly denied any knowledge of the accounting fraud that Enron officials used to misstate its earnings and debt prior to its collapse in December 2001.
Accounting firm collapses
The probe into the 2001 collapse of Enron, at the time the seventh-largest US company, has led to criminal charges against 28 people and put Enron's former accounting firm, Arthur Andersen LLP, out of business.
In Skilling's expected indictment, prosecutors are relying in part on information provided by former Enron executives Andrew Fastow and David Delainey, who pleaded guilty to conspiracy and insider trading in January and October, respectively, The Washington Post reported on Thursday.
In particular, the daily said the Justice Department's Enron Task Force and regulators at the Securities and Exchange Commission had focused on Skilling's statement to the US Congress in 2002 that Enron was on solid financial ground when he resigned from the company in August 2001, just months before the company's collapse.
Skilling is the highest-profile former Enron executive to date to face criminal charges and the 28th to be charged over the scandal.
Top executives including Skilling pocketed millions of dollars from sales of stock prosecutors alleged was inflated.