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Massachusetts education officials have overstated the number of students on waiting lists for charter schools and have stumbled in other ways in overseeing the schools, such as applying uneven standards for renewing their operating licenses, according to a state audit released Thursday.

The audit also raised questions about the accuracy of data that education officials routinely collect from charter schools and local districts; such data are self-reported with little verification by the state. That makes it difficult to fully judge charter schools’ performance, the auditor’s office said.

“Lawmakers need sound information with which to make decisions,” state Auditor Suzanne M. Bump said in a statement. “Charter school demand is one area where reliable calculations are required. Of even greater relevance, however, is the reliability of the data used to define equity between the parallel systems of district schools and charter schools and to compare educational outcomes.”

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The findings were among the most notable deficiencies in an audit that largely found that state education officials were doing an effective job in overseeing the 81 charter schools in Massachusetts. The audit examined a period from July 2009 to June 2013.

Mitchell Chester, the state commissioner of elementary and secondary education, said he agreed with some of the findings but disputed others. For instance, Chester defended the state’s calculation of waiting-list numbers and said the state uses a uniform set of standards in judging the renewal of charter schools.

He also denied that there are accuracy problems with data collected from local schools, which he pointed out are government agencies that verify their own data. Putting that responsibility in the state’s hand, he said, would require a huge bureaucracy.

But Chester agreed with the recommendation for the education department to upgrade its data-collection systems, noting some are more than a decade old, but stressed there have been no data breaches.

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“I welcome the report,” he said. “I am committed to continuous improvement.”

The highlighted problems, especially the waiting list numbers, are expected to provide ammunition for critics of charter schools as they wage another fight against attempts by advocates to raise a state-imposed limit on the number of independently run charter schools that can operate.

Advocates are weighing whether to pursue a ballot question in 2016, after the state Senate overwhelmingly rejected legislation last summer to increase the cap. Supporters of more charter schools often point to the growing numbers on waiting lists.

But those numbers have been increasingly drawn into question. A Globe review last year found the state inflated the number of students on charter school waiting lists, which had totaled 53,000 students statewide.

At the time, the state simply added up the number of students on waiting lists at individual charter schools without checking for any duplication. Often, students apply to more than one school and show up on multiple waiting lists.

The state has since changed its methodology, collecting the names of students on the waiting lists and counting them just once for a statewide tally, which shrank to 40,000 as duplicated names were crossed out.

The audit, however, found another 2,000 students who were counted more than once, reducing the tally to 38,000.

The audit urged the state to more closely scrutinize the lists for duplications. It also suggested the state stop letting schools keep students on waiting lists for more than one year — a practice that could artificially inflate numbers as some of those students may no longer be interested in attending.

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Chester said the state education board has been proactive on this front, noting the board voted to not allow charter schools to roll over their waiting lists from one year to another. He said he thought the audit overstated the problem.

“The fact that the auditor questioned 2,000 out of 40,000 names on the waiting list is not very substantial,” said Chester, also noting that waiting list numbers change frequently as seats open up.

Marc Kenen, executive director of the Massachusetts Charter Public School Association, said that waiting list numbers still show that more charter schools are needed.

“We are glad the audit has validated tremendous demand for charter schools,” he said.

Mary Battenfeld, a member of QUEST, a grass-roots parent organization in Boston concerned about charter school expansion, said problems with the waiting list numbers are just the tip of the iceberg.

“To me, I found a lot of troubling, but not surprising, information in the audit,” she said.


James Vaznis can be reached at jvaznis@globe.com. Follow him on Twitter @globevaznis.