Twenty-one percent of students statewide in grades three through eight eligible to take Common Core tests boycotted the exams in April, the state Education Department said Friday — a level similar to the national record-setting number of test refusals in spring 2015.

Passing rates, meanwhile, rose on both tests over the year before, though more in English language arts than in math, the department said.

Among about 900,000 students who took the exams, 37.9 percent scored at levels of proficiency on the ELA, up 6.6 percentage points, and 39.1 percent on the math test, up 1 percentage point. The math scores, however, exclude thousands of accelerated students who decided to take the high school Regents algebra exam rather than the eighth-grade math test.

Education Commissioner MaryEllen Elia, in a hastily called afternoon conference call with reporters, said because of changes made to this year’s exam and testing environment, the 2016 test scores and data were not an “apples-to-apples” comparison with previous years.

Betty Rosa, chancellor of the state Board of Regents, which sets education policy, said in a statement, “We made important changes to the assessments this year and we’re going to continue to look at ways to make them even better moving forward. While it’s not possible to make direct comparisons of this year’s results to past years, I’m cautiously optimistic the changes we’re making will drive improvements in teaching and learning.”

Rosa, who was elected in March, has sympathized with parents wrestling with the decision of whether their children should sit for the exams, saying she would have her own kids opt out if she were acting simply as a parent.

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This was the fourth consecutive year of test refusals linked to state-driven education reforms. A year ago, the Education Department estimated the number of test refusals at 200,000 students statewide in grades three through eight, with about 35 percent of those on Long Island.

As part of an effort to address parents’ and educators’ ire over the controversial tests, the state this year trimmed the number of questions and students did not face a time limit. The Regents also set a four-year moratorium on usage of scores that means they cannot be used punitively against students or teachers, whose performance evaluations are by law linked to the results.

Critics of the Common Core tests and other reforms were not impressed with the scores released Friday.

Carol Burris, executive director of the Queens-based nonprofit Network for Public Education and a former principal of South Side High School in the Rockville Centre district, said of the English scores: “That kind of an increase was expected because so many kids were complaining they were not able to finish the test. Does that mean the kids in New York State learned more this year? Probably not.” She called the math bump statewide “a very tiny increase.”

For Long Island’s students, averages of student performance in Nassau and Suffolk districts showed percentage increases in each grade over 2015’s results, on both the ELA and the math tests, according to Newsday’s calculations from state data released Friday.

For example, the average passing rate for third-graders in Nassau County districts on the English test was 60 percent; last year, the figure was 43 percent. For third-graders in Suffolk County systems, the average passing rate on the ELA was 49 percent, well above the 30.4 percent in 2015.

Statewide, black and Latino students made progress on ELA proficiency compared with last year, the Education Department said.

Black students saw a 7.7 percentage-point increase in those achieving proficiency, while Latino students had a 7.1 percentage-point increase. In both cases, the increases were greater than those seen by white students, whose scores showed a 5.6 percentage-point increase statewide.

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As a result, the agency said, the achievement gap in ELA that historically has separated the proficiency of black and Latino students from their white peers closed slightly statewide. Proficiency on the math exam statewide and in New York City this year also increased for black and Latino students in math, though less than on the English test.

Officials said the data also revealed that proficiency on the ELA increased the most this year among third- and fourth-graders.

Elia credited various factors with contributing to that jump — among them that those students had received instruction in the Common Core-related learning standards since kindergarten and first grade, and teachers have had an additional year of experience with the curriculum.

The commissioner on Friday described the test-refusal numbers as essentially “flat.”

A change in the way the department calculated refusals gave a truer number of students who did not take the exam, Elia said. About half of those who did not take the exams this year were new refusals, though she noted that meant that half who refused last year opted back in.

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Still, in the Island’s 124 public school districts, more than 50 percent of students eligible to take the exams boycotted them, according to Newsday surveys of districts that drew responses from 100-plus systems. The newspaper’s surveys last year showed more than 46 percent of the region’s eligible students opted out.

The Island has been the epicenter of the opt-out movement in New York, which began with grassroots activism by parents and educators upset with tougher tests aligned with the Common Core standards, and spread through social media and community forums.

“When she said it was flat, I disagree, considering the full-court-press she put on . . . to convince parents not to do what they feel is in the best interest of their children,” said Jeanette Deutermann, a North Bellmore parent of two and founder of Long Island Opt-Out, a regional group that has spearheaded the movement. “We have been very clear: We want a complete overhaul — testing, curriculum, standards, data collection — and we will not accept anything else.”

For the second-straight year, the state data showed Plainedge was the Nassau school district with the highest percentage of refusals on both tests, while Comsewogue’s opt-out percentage was the greatest among Suffolk County districts on both exams.

The leaders of High Achievement New York, a Manhattan-based coalition of business groups and others that support Common Core standards, hailed the increase in proficiency scores and noted the plateau of those opting out.

“The rise in scores proves that the combination of high standards and aligned assessments are working — students across the state are finally being prepared for 21st-century careers and challenges. But it also means that students who opt out are falling further and further behind their peers,” said Stephen Sigmund, the group’s executive director. “Now is the time to come together to strengthen the assessments, continue to reduce opt-outs and make sure that every child receives a great education.”

Earlier this month, U.S. Education Secretary John B. King Jr. pushed new draft regulations that would designate public schools in which large numbers of students refuse to take Common Core tests as in need of improvement.

The proposals drew criticism from those in New York who have opposed the tougher exams and other education reforms, which King championed when he was New York’s education commissioner.