WASHINGTON—Federal regulators on Thursday filed civil charges against former MF Global Holdings Ltd. Chief Executive Jon S. Corzine and a top lieutenant for overseeing the misuse of almost $1 billion in customer funds, saying Mr. Corzine "bears responsibility" for the New York commodities brokerage's 2011 demise.

The Commodity Futures Trading Commission's complaint cited conversations not previously disclosed purportedly showing Mr. Corzine played a more active role in the firm's activities than he had suggested in the past.

The lawsuit, filed in U.S. District Court in Manhattan, comes as a new blow for Mr. Corzine, whose reputation—built on a career as a top executive at Goldman Sachs Group Inc., New Jersey governor and U.S. senator—has been tarnished in the past two years. Mr. Corzine, 66 years old, has been grilled by Congress in several high-profile hearings and is the focus of several civil lawsuits related to his oversight of the company.

The agency also charged a former executive at the firm, Edith O'Brien, with misusing customer funds, saying she aided and abetted the violations. The agency is seeking monetary penalties from Mr. Corzine and Ms. O'Brien and to ban the two from ever again trading commodities on Wall Street.

The CFTC's 47-page complaint depicts Mr. Corzine as instrumental in making decisions that put customer accounts at risk by allegedly moving money in violation of strict rules prohibiting such transfers.