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.