MF Global took futures segregated money and put it into the account for customer securities, essentially mixing futures and securities that were both owned by customers, said an official familiar with the matter.
Until now, it was believed that only customer futures accounts were affected.
The source also told Reuters that MF Global had been using customer funds for "several days if not weeks" rather than just a few days before the firm collapsed.
Regulators had previously thought the firm was using customer funds on the Thursday and Friday before it filed for bankruptcy on October 31.
CME Group, the Chicago exchange where MF Global traded, said it had reviewed the company's books a week before the bankruptcy and found no issues with the customer money.
If MF Global started improperly dipping into its customers' accounts long before the firm's collapse, the allegation would raise questions of why the regulators and auditors failed to spot such behaviour.