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The state’s education commissioner declared two high schools in Boston and an elementary school in Fall River “underperforming” Monday, citing years of low state standardized test scores.

The designations mean that Brighton and Excel high schools in Boston and the Mary Fonseca Elementary School in Fall River will have to undergo major restructuring if they want to avoid state receivership in three years. Changes could include replacing teachers and administrators, lengthening the school day, and bringing in new instructional techniques.

During a press briefing, Mitchell Chester, the state commissioner of elementary and secondary education, called the low MCAS scores and graduation rates at Brighton and Excel “distressing.”

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“Students are not getting the education that will prepare them well for success after high school,” Chester said.

Chester made the announcement as he released the latest round of standardized test scores for schools across the state, which showed stagnant results on the make-it-or-break-it 10th-grade exams that students must pass in order to graduate.

In English, 91 percent of 10th-graders scored proficient or higher, the same as last year. In math, 78 percent of students scored proficient or higher, a one percentage point drop from the previous year, while in science, scores rose one percentage point to 73 percent.

In a way, the day marked the end of an era for the Massachusetts Comprehensive Assessment System. After 18 years of being a paper-and-pencil test, the state is moving the exams online next spring, starting with those for grades 3-8.

In preparation for that, nearly three-quarters of all students in those grades statewide tried out a different test this year, known as the PARCC, which is the inspiration for the new tests. Most of the students took those tests on the Web, while students at other schools stuck with the traditional MCAS.

Consequently, the state did not produce statewide results for students in grades 3-8 in English and math.

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The new tests, nevertheless, generated controversy as a number of families seized upon the experiment to voice their opposition to standardized testing. Parents either refused to let their children take the tests or students opted out on their own.

Such protests played a role in Boston Latin School and the Roger Clap Innovation School sliding from the highly-desirable Level 1 status, under the state’s accountability status, to Level 2, according to Mayor Martin J. Walsh, who blasted Chester over the airwaves Monday for downgrading the schools’ ratings.

“It’s completely wrong,” Walsh told hosts on Boston Herald Radio.

Boston Latin Academy also dropped to Level 2 status, but the School Department chalked that up to students merely being absent and made no mention of testing protests.

Testing participation rates for all students as well as various demographic groups must be 95 percent or higher.

Carrie Weatherhead, a Dorchester mother, said she felt awful that her son was one of two students at the Clap who opted out of the tests. With only 29 Latino students being tested, that was enough for the tiny school’s participation rate to fall below the 95 percent threshold for that demographic group.

“I feel bad for the school because I feel like it’s my fault,” said Weatherhead.

She said the superintendent’s office and the school’s principal said the opt out would not hurt the school’s rating. If her son had known it would, she said, he would have taken the test.

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Chester defended the decision to downgrade the schools, noting that state and federal law require the testing of students.

The Education Department downgraded 41 schools because of low test participation, but Chester said low participation had been a problem at some schools before the protests began, meaning other issues could be at play.

Boston school officials said in a statement they intend to appeal the lower designations.

Monday’s announcement included some bright spots. The state gave commendations to 49 schools for high achievement or for closing gaps in performance among students of different backgrounds. The list included the Mozart Elementary School in Roslindale and three schools in East Boston: the McKay K-8, Bradley Elementary, and Patrick Kennedy Elementary.

The Brooke Charter School in East Boston also received the same recognition.

The state also removed the “underperforming” designations from three schools: Bentley Academy Horace Mann Charter School in Salem, Spark Academy in Lawrence, and William DeBerry Elementary School in Springfield.

But given that the state declared three new schools underperforming, the number of schools carrying that designation statewide remains at 33.

And Chester said two of those schools — the Mattahunt Elementary in Mattapan and the High School of Commerce in Springfield — could go into receivership in a year if the districts cannot come up with plans to turnaround lackluster improvement efforts thus far. The state has taken that action at four other schools, including two in Boston, in recent years.

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Springfield Superintendent Daniel Warwick expressed a willingness to work with the state on the review.

“We are eager to find new pathways to success to build on the gains that Commerce has experienced over the past couple of years,” Warwick said in a statement.

The Boston School Department said in a statement that it was awaiting the next steps from the state. It also said it would work closely with Brighton and Excel high schools to craft plans “that will rapidly accelerate the learning and achievement of their students.”

English High School in Jamaica Plain had been hoping to finally shed its underperforming designation this year, but Chester decided against the move. Although MCAS scores are higher than in many past years, the school’s graduation rate is barely above 50 percent.

“English High School deserves a lot of credit for the progress the school has made,” Chester said. “It’s in a much better place, but the challenge for me is the graduation rate remains low.”

James Vaznis can be reached at jvaznis@globe.com.