Hundreds of millions of dollars are still missing from customer accounts at MF Global Holdings Ltd., according to people familiar with the matter.

On Friday, MF Global said it had discovered $659 million in customer funds in one of its accounts at J.P. Morgan Chase & Co. that it hadn't been able to locate while scrambling to avoid bankruptcy. The implication was that there was no meaningful shortfall in client funds.

That turns out not to be the case, say people familiar with the matter. As of Friday, $593 million remained missing from customer trading accounts, according to a person familiar with the regulatory probe of the collapsed firm.

Commodity Futures Trading Commissioner Bart Chilton said in an interview Saturday that the funds in the J.P. Morgan accounts had already been accounted for as the regulator pored over MF Global's books in the past week.

'It's not like we looked behind a couch cushion and were like, 'oh, there it is,' ' he said.

The confusion, which comes nearly a week after the firm moved to declare bankruptcy, highlights the tangled nature of MF Global's chaotic bankruptcy and heightens the mystery behind the firm's accounting. The shortfall in customer accounts, initially estimated at about $900 million, scuttled a last-minute deal last weekend with brokerage firm Interactive Brokers Group Inc.

Ever since, regulators, traders, MF Global customers and exchanges have been trying to learn what happened to the missing funds, which MF Global held in trading accounts for clients.

For a brief time Friday, it seemed as if MF Global might have uncovered the funds at J.P. Morgan, which housed the firm's client balances. MF Global believed the proceeds from some last-minute trades were stuck at J.P. Morgan when the firm filed for bankruptcy on Monday.

J.P. Morgan said in a statement Friday that it didn't have any information 'as to whether any such balances are related in any way to the 'missing' customer funds.'

A person familiar with the matter said MF Global still hasn't had a full accounting of its holdings at J.P. Morgan. MF Global has maintained that it didn't mislead anyone and that it suffered from a chaotic environment in which its accounts were slow to settle in the days leading up to its collapse.

Meanwhile, CFTC Chairman Gary Gensler has stepped away from the MF Global investigation in order to remove any perception of a conflict of interest that could arise due to his long standing ties to Jon Corzine, who resigned Friday as CEO of MF Global. Mr. Gensler worked at Goldman Sachs Group Inc. when Mr. Corzine was running it in the 1990s.