The Los Angeles school district paid $200 million more in salaries than it budgeted last year even as it laid off 2,000 teachers and hundreds of other employees, according to an internal audit.

Auditors so far have unearthed no wrongdoing, but officials are puzzled, concerned and perhaps even a little embarrassed.

“We’ve been in the process of cleaning it up,” said L.A. schools Supt. Ramon C. Cortines, who said his staff is verifying the size of the discrepancy and will, over time, determine how much relates to incomplete accounting and how much to something more serious.

The issue emerged in an audit, completed in December, on the arcane subject of “position control.”

It looked at how well the Los Angeles Unified School District keeps track of salaried positions.

Not well, concluded auditors working for the district’s inspector general.

“The system is broken,” said Inspector General Jerry Thornton.

“We really don’t have adequate position control and we don’t know where our funding comes from for all these positions,” Thornton said.

He added: “There’s no suggestion of impropriety or fraud. We didn’t see people being paid who aren’t working or who aren’t there.”

Last year, the district listed 76,860 full-time positions, which were supposed to cost $4.7 billion. Instead, the district spent $4.9 billion.

Auditors have yet to identify where the bulk of the difference came from or to whom it went.

In some cases, unfunded or expired positions remained on the payroll. In others, jobs that persisted on the payroll turned out to be vacant. Problems turned up with about 3,000 positions.

The audit results are the latest painful addendum to a payroll debacle that resulted in thousands of employees being under- or overpaid starting in January 2007.

In this instance, the high-tech but poorly configured new payroll system was supposed to catch salary irregularities, but that feature was never installed.

Some of the latest problems emerged as the cash-strapped district was determining which employees to lay off, based on job duties and seniority.

On June 20, 2009, the budget services division identified more than 900 unfunded positions that accounted for about $30 million of unbudgeted money that had been spent.

howard.blume@latimes.com