The Department of Education’s annual assessments of how much space is available in each school building are not always correct.

That’s according to an audit being released today by Comptroller John Liu, who is in the midst of scrutinizing DOE data in a series of reports. Liu, who is weighing a 2013 mayoral run, launched the audits this spring after holding town hall meetings in which New Yorkers suggested topics for investigation. Last week, he critiqued the DOE’s handling of the Absent Teacher Reserve, and he has at least three other schools audits in the works.

The newest audit examines the city’s “Blue Book,” which contains space estimates for each school building. The DOE and the School Construction Authority use the Blue Book to guide how many students can be placed in a school, and how many schools can fit into a building. Critics, including members of the City Council, say Blue Book numbers don’t always reflect reality — for example, suggesting that an additional class could fit into an art room — and that decisions based on them can leave schools crunched for space.

To evaluate the city’s success at ensuring accurate Blue Book data, Liu’s office analyzed entries for 23 schools and found that space assessments for 10 percent of all rooms were incorrect in a way that affected the school’s overall capacity.

“Proper space is essential for fostering a good learning environment, yet all too often the DOE is basing critical building decisions on its unreliable Blue Book, which bears too much resemblance to a house of cards,” Liu said in a statement.

In a response, Kathleen Grimm, the DOE’s deputy chancellor in charge of space, counters that overall, estimates for the 23 schools were spot on: There are just as many seats available in the schools as the department said, even if there are some estimation errors within some of the schools.

But Liu’s office argues that looking at the big picture gives short shrift to inaccuracies in space assessments at the school level.

“DOE’s and SCA’s methodology only makes sense if the goal is to match total seats with total enrollment within the system,” the audit says. “As the data is used to make decisions regarding individual schools and groups of schools, the best reflection of the accuracy of the Blue Book is the error rate of each individual school.”

The audit makes several recommendations and the DOE has signed on to most. They include making principals more aware of how important it is for them to complete an annual space survey accurately, ensuring that errors in space estimates are corrected, and checking how rooms are used during visits to verify the information that principals report.

But the city rejected two of Liu’s recommendations: to create and publish information about space availability in schools and to use the Blue Book “more effectively” to identify schools that are overcrowded.

That’s because those things are already happening, DOE and SCA respond within the audit. “We do not believe the findings in the Audit Report remotely support the Comptroller’s implication that the SCA and DOE do not effectively use the Blue Book as a starting point to identify over-utilized schools,” they said.

“The Blue Book is one source of information that informs school construction and building decisions, and the Comptroller’s report acknowledges that the DOE appropriately uses the book in conjunction with other sources of information,” DOE spokeswoman Barbara Morgan said in a statement.

Liu’s full audit and the DOE’s full response are below.