Where did $1 million of seized money go?

A million dollars appears to be missing in records of San Diego Police Department funds seized from drug runners and other criminals, and the department is seeking an audit after U-T Watchdog spotted the issue.

Under a program that directs seized assets to local law enforcement agencies, the police force receives money from the U.S. Treasury Department. The Watchdog identified the missing money in reviewing records of the program over the past five years.

The certification report San Diego police submitted to the federal government in 2010 showed a closing balance of $1,153,426.

For 2011, the same report showed a beginning balance of $153,426 — exactly $1 million less than the prior year — with no explanation.

The funds in question came from assets seized by Treasury agencies including Internal Revenue Service, Customs and Border Protection and the Secret Service. Local agencies also receive funds from the Department of Justice when assets are seized by the Federal Bureau of Investigation, the Drug Enforcement Administration and other agencies.

Over the past five years, San Diego police received $6.4 million from the Justice and Treasury programs.

The U-T has been reporting on spending through such programs in jurisdictions across the region since April. The Watchdog received the San Diego police program records on May 14, and asked the next day about the $1 million inconsistency.

On Thursday, spokesman Lt. Kevin Mayer issued a brief statement saying the matter was being referred to financial investigators at City Hall.

“We acknowledge you have noted a discrepancy,” Mayer wrote. “We have asked the City Comptroller to do a complete review and audit of the seized asset fund to see if there is an error.”

The Treasury Department declined to discuss what ramifications there might be for the San Diego Police Department. Officials issued a statement saying the government has measures in place to make sure program participants comply with federal rules over how the funds may be used.

“Instances where misuse or mis-accounting of funds may have occurred are referred to the Treasury’s Office of Inspector General for further action where appropriate,” the department wrote in a statement.

Federal officials do take action when funds are found to be mishandled.

The Watchdog reported earlier this month that the San Diego County District Attorney’s Office will lose out on certain future grants after spending $30,000 on a state prosecutors’ professional association — not an allowed expense under the federal program.

Federal rules dictate how the seized assets can be spent. Generally they must be used for law enforcement support projects; a percentage may be donated to nonprofit community-service groups.

Most of the money the San Diego Police Department received came from the Justice Department — between $650,000 and $1.7 million each year for five years.

Almost $2 million was spent on unspecified building and improvements in 2011, the department reported. Most of the rest paid for gas, insurance and other costs related to police helicopters.