Less than a year into his tenure as Florida’s education commissioner, Tony Bennett resigned Thursday amid a controversy over adjustments he made to school grades last year as Indiana’s school chief.

The Associated Press published e-mails this week suggesting Mr. Bennett tweaked a new A-F grading system in Indiana to favor a charter school run by a major Republican donor – giving it an A instead of the initial C. Bennett said in a press conference that the accusation was “malicious and unfounded” and that he hoped there would be an investigation, but that he was resigning to avoid distraction to Gov. Rick Scott’s education reform efforts in Florida.

Bennett has been a prominent member of Chiefs for Change, a coalition of reform-minded state school chiefs backed by former Florida Gov. Jeb Bush, which put out statements of support for him this week. As an outspoken promoter of a certain brand of accountability, Bennett’s supporters see him under attack by politically motivated opponents.

“The most important thing we ought to do is educate children,” Bennett said Thursday, adding that he wished complex education policies could be discussed “without getting personal or assigning motive.”

But the pressure for him to resign is just one example of people’s “growing concern that there is little or no honesty or integrity when measuring the performance of schools,” says Maria Ferguson, executive director of the Center on Education Policy at George Washington University. There’s an “unrealistic” pressure on people to change public schools quickly, Ms. Ferguson adds. The public expects “some brave person to wave a sword,” but then that “can pressure human beings to do stupid things” to try to fulfill those expectations.

How schools are measured often has high stakes attached to it. In Indiana, the grades affect funding, determine if schools were taken over by the state, and have implications for whether students can seek private vouchers immediately or have to attend public school for a year first.

In one of Bennett’s e-mails last fall that was revealed this week, he wrote to his chief of staff after learning about Christel House charter school being likely to receive a bad grade: “This will be a HUGE problem for us…. They need to understand that anything less than an A for Christel House compromises all of our accountability work.”

Bennett explained in an interview with Rick Hess of the American Enterprise Institute this week that finding out that an otherwise high-performing school was slated to get a C prompted him to look at the grading system and realize it unfairly penalized Christel House and another dozen schools that didn’t have 11th and 12th grades in their structure. He said they adjusted for all those schools to account for that. For years, Christel House had been performing well with a challenging student population.

Christel House provides education around the world and was founded by Christel DeHaan, the political donor who has been characterized by press reports as a Republican donor. Bennett told Mr. Hess he has donated to both parties.

The Associated Press reports that the C grade that initially came in for Christel House was due to low 10th-grade algebra scores.

The American Federation of Teachers in Indiana issued a call Thursday afternoon for the state to suspend its A-F school grading system.

Bennett has been involved in revising Florida’s A-F grading system, including persuading a split board of education to adopt a “safety net” so that the grades of more than 500 schools would not drop more than one letter grade this year.

The controversy has the potential to “open up new conversations about what goes into these grades,” says Michael Petrilli, an education analyst and executive vice president of the Thomas B. Fordham Institute in Washington. “It’s not a science. There are a lot of judgments and we should talk publicly about the pros and cons and the tradeoffs.”

With a single letter grade, “you lose a lot of nuance and it’s not going to be fair for every school,” Mr. Petrilli says. On the other hand, some states dump too much data in parents’ laps and “you’d need a PhD to make sense of it.”

This case particularly raises questions about putting high stakes on school grades, Petrilli says. States need to be transparent and be very sure if it’s going to give a school an F. “I’m not confident all the [state] school grading systems have gotten it right.”

Many of the waiver applications that states have been submitting to the US Department of Education to free themselves from some components of the federal No Child Left Behind law are long and dense, and there’s “so much potential for subterfuge,” says Ferguson of the Center on Education Policy.

More efforts are needed to “win hearts and minds,” she says, to help people understand why states are shifting to common core standards, new assessments, and new grading systems for individuals and schools, and to reassure them it will be done in a way that watchdogs can witness and critique.

Bennett wished Florida success in its endeavors and vowed Thursday to “continue to be one of the nation’s most ardent supporters of college and career ready standards. They are the right policy."

He has been serving on the governing board of the Partnership for Assessment of Readiness for College and Careers, one of two prominent coalitions developing assessments aligned with the Common Core State Standards. Indiana and several other states have backed out of their participation in PARCC and Florida has been considering whether to remain committed.

• Associated Press material was used in this report.