An audit by Comptroller John Liu’s office found that the Department of Education overpaid for food about .003 percent of the time two years ago.

Liu’s latest DOE audit looked at the way the Office of SchoolFood contracts and pays vendors for food that is served in schools — at about 850,000 meals annually, according to the city. It concludes that of the $113.9 million spent on school food in the 2009-2010 school year, more than $400,000 could be recouped because records showed the city had paid too much or because there was no record that the city had received any food at all.

The DOE is paying an 862 percent markup for fresh parsley and more than 400 percent the real cost of several other vegetables and herbs, according to a spreadsheet that Liu’s office compiled. The department is paying more than the real value for 76 kinds of food, according to the spreadsheet.

An even broader issue, according to the audit, is that department doesn’t always check when contractors says they require payment or have made deliveries.

“The DOE paid $113 million for which it got receipts, but never looked inside the bags to see if the groceries were there,” said Matthew Sweeney, a Liu spokesman, in a statement.

The audit urges the city to tighten controls over school food spending.

Last time Liu’s office released the results of a DOE audit, about the use of pre-kindergarten funds, department officials said they were submitting their response “under protest.” But Eric Goldstein, head of the Office of SchoolFood, signaled no such resistance in a letter accompanying the DOE’s response to today’s audit.

“While their findings were quantitatively insignificant relative to the scale of our operations, several points raised were of interest and will provide us opportunities to further improve our operations,” Goldstein wrote.

He said the department already took many of the steps the audit urged but would look for other ways to ensure that prices paid for school food are fair and reasonable.

Today’s audit is part of an ongoing series of DOE audits that Liu initiated this spring after holding town hall meetings in which New Yorkers suggested topics for investigation. Long considered a potential 2013 mayoral contender, Liu has seen his prospects in that race effectively collapse amid revelations about its fundraising practices.

Pricing is only one of the Office of SchoolFood’s concerns. In May, we reported that some food served in cafeterias does not meet the city’s own nutrition guidelines it set last year for bake sale snacks.

Here’s the audit that Liu’s office released today:

And here’s the DOE’s response: