Federal regulators have ordered an audit of every American futures trading firm to verify that customer money is protected, a move that comes after roughly $600 million in client funds went missing from MF Global, the bankrupt brokerage firm once run by Jon S. Corzine.

The Commodity Futures Trading Commission, the federal regulator searching for the missing money at MF Global, will audit many of the nation’s largest futures commission merchants, according to a person briefed on the mater. Exchanges like the CME Group will examine smaller firms to ensure they are keeping customer money separate from company money, a fundamental rule on Wall Street.

The regulator also announced on Thursday that it had formally opened an investigation into MF Global, a largely symbolic move that indicates the seriousness of the case. The agency has already issued subpoenas to MF Global and its auditors, PricewaterhouseCoopers, but the commission had to vote before announcing a full-scale investigation.

“The commission has determined it is in the public interest to confirm the existence of this particular investigation,” the agency said in a statement.

Gary Gensler, the commission’s chairman, abstained from voting after recusing himself from the investigation. He stepped back from the case amid questions about his past acquaintance with Mr. Corzine. While the two were not close in recent years, Mr. Gensler worked for Mr. Corzine at Goldman Sachs in the 1990s. And Mr. Gensler had supported Mr. Corzine’s campaign as a Democratic candidate for governor of New Jersey, with a $10,000 check.

With Mr. Gensler out, a Republican member of the agency, Jill E. Sommers, will serve as the senior commissioner on the case, the agency said in the statement.

“Segregation of customer funds is at the core of customer protection in the commodity futures and options markets and must be maintained at all times,” Ms. Sommers said in the statement. “I have complete confidence in the dedicated men and women in enforcement to carry out the necessary investigation to get to the bottom of what happened.”

The commission and other federal regulators are continuing to search for the $600 million missing from MF Global. The Federal Bureau of Investigation is also investigating.

Mr. Corzine and MF Global have not been accused of any wrongdoing.

The futures industry has boomed in recent years, growing to more than 100 futures commission merchants in the United States. Most Wall Street powerhouses, including Goldman Sachs and JPMorgan Chase, feature a futures business, as do many boutique banks and brokerage firms.

The regulator’s decision to audit every futures firm is aimed at restoring calm, and perhaps faith, to a jittery industry. MF Global’s downfall, and the revelation of missing customer money, has raised questions about the safety of the futures business.

MF Global’s customers, including farmers and traders, were frozen out of trading by the CME Group on the day MF Global filed for Chapter 11. Many customers are now angry at CME, the exchange where MF Global did business, for not catching the missing money sooner.

The last large-scale audit the CME conducted at MF Global was in January. It also did a “spot audit” on Oct. 26 to verify that customer money was in the right accounts at outside banks, said a person close to the CME who did not want to be identified because the investigation was continuing. MF Global filed for bankruptcy on Oct. 31.

On Nov. 2, the exchange said MF Global might have transferred client money “in a manner that may have been designed to avoid detection,” a serious violation of Wall Street regulations.