The U.S. Securities and Exchange Commission sided with the Lehman Brothers Holdings Inc. brokerage in a $3 billion dispute over assets with Barclays Plc, saying a judge ruled correctly that the U.K.’s claim to securities in customer reserve accounts was conditional.

If the SEC prevails, Barclays may lose its claim to as much as $1.3 billion reserved for customers, according to an SEC court filing yesterday.

Michael O’Looney, a Barclays spokesman, declined to comment on the SEC filing.

Barclays and Lehman Brothers Inc. both appealed U.S. Bankruptcy Judge James Peck’s ruling that told Barclays to return $2 billion in margin assets to the bankrupt brokerage, and said it had “only a conditional right” to $769 million in the customer reserve account. Brokerage trustee James Giddens is fighting Peck’s order to give the bank at least $1.1 billion, and possibly the $769 million, if it leaves enough in the reserve account to satisfy remaining customer claims.

As much as $1.3 billion in reserve assets can’t go to Barclays if customers suffer as a result, and Giddens has said he needs the assets to satisfy claims, the SEC said in the filing. In addition to the $769 million, a second pool of funds, $507 million in margin for customer transactions at the Options Clearing Corp., raises similar issues, the SEC said.

SEC Notice

SEC staff members told both parties in 2008 when Barclays bought Lehman’s North American business that they might violate a customer protection rule if Barclays took the assets, according to the filing.

The dueling between London-based Barclays and trustee Giddens follows a bankruptcy court trial held in 2010 before Peck in Manhattan. Both sides are due to file court papers today in their appeals.

The district court case is Giddens v. Barclays Capital Inc., 11-cv-06052, U.S. District Court, Southern District of New York (Manhattan).