Alonso said he also was disappointed that he couldn't report double-digit increases to a city that had rallied its poor, minority students through years of against-the-odds successes.
"The story of growth over time is not diminished — it's indubitable," he said. "I didn't place a monitor in every school to find schools cheating. … I wanted to say that the progress is real."
The 2011 scores place the city even further below the state average, and further from catching up.
The MSA was administered to 365,000 students throughout the state in grades three through eight. The test fulfills the federally mandated No Child Left Behind Act, used to determine if students of all sub-groups are making adequate yearly progress. The law requires that 100 percent of students score proficient in reading and math by 2014.
Maryland elementary and middle school students continued a strong eight-year trend of making steady progress on the tests, noting gains in reading and math on this year's assessments.
The state's elementary school students are nearing 90 percent proficiency marks on state reading assessments, after noting a small gain from last year to 88 percent. The number of students scoring proficient on elementary school math tests remained flat at 86 percent.
In middle school, the percentage of students scoring at proficient levels in math and reading also rose slightly. Proficiency levels in middle school reading rose to 84 percent, and mathematics rose to 74 percent.
Though scores remain fairly steady in the 80s and 90s in surrounding counties, significantly fewer schools made adequate yearly progress targets set under federal law. School leaders blamed the rising goals of No Child Left Behind. The trend was consistent throughout the state.
Baltimore County schools made slight improvements in both reading and math at most grade levels measured by the MSA, taking steps back only in sixth-grade reading and eighth-grade math. Preliminary numbers showed 22 schools failing to make the progress goals for the first time and 21 in school improvement, officials said.
In her last release of the state's MSA results, state school Superintendent Nancy S. Grasmick said the results of the state assessments demonstrated that "the state continues to do incredible work on behalf of its students."
While 258 schools failed to meet annual yearly targets for the first time this year, a number of schools in several districts have 90 percent or more of their students making proficient or advanced marks, state officials said.
Grasmick, who will retire Thursday after leading the state to a No. 1 ranking by Education Week three years in a row, attributed strengthening instruction statewide to the stark uptick in the number of students scoring at advanced levels, when compared to 2003.
This year, the proportion of elementary school students reading at advanced levels is 35 percent, more than double the share eight years ago. More than half of the number of middle school students who are proficient in reading are also at an advanced level. Both groups noted similar gains in advanced mathematics marks, though Grasmick said that middle school math still needs improvements.
"We want to accelerate rather than stay stable," she said.
She said the state found districts that struggled this year were those undergoing system-wide transformations. "I think until all of the structures are in place, sometimes the instructional programs are not front and center," Grasmick said.
Grasmick said that the state also needs to continue to work toward closing the achievement gaps.
But, in this time of emphasizing greater accountability, state officials find themselves in the odd position of being unable to release as much testing data as they have in previous years.
That's because federal regulators say the privacy of individual students could be compromised by test results released for very small sub-groups.
If a school only has eight special education students in the third grade, for example, a parent of one of those students could deduce, based on reported results, what the other students in the group scored on a test. That means this year's results won't include specific numbers for many small sub-groups and that, in some cases, the public might not learn where a school failed to make adequate yearly progress.
"It will be a concern at the school level," said a state Department of Education spokesman, Bill Reinhard. "At the system level, not really."
Leslie Wilson, the state's director of testing, said that for several years, she did not believe the federal government intended to enforce the Family Educational Rights and Privacy Act in this way.
But then, one of her colleagues attended a conference where Maryland's testing website was used as an example of what not to do. Later, a technical advisory team from the U.S. Department of Education came to Maryland to tell state officials how to bring their website into compliance.
The greatest absurdity might lie ahead. According to No Child Left Behind, the goal for all schools is 100 percent proficiency by 2014. But privacy regulations would prevent reporting of this achievement, because it would let the public know that every individual student scored well on the test.
"It seems so ludicrous," Wilson said.
An earlier version of this story reported an incorrect number of city schools that recorded drops of more than 20 percentage points in reading or math, or both subjects. Also, the total number of city schools that have been referred to the state for cheating investigations was incorrect. Eight have been referred this year, in addition to four schools already under investigation, for a total of 12. The Sun regrets the errors.
Baltimore Sun reporters Childs Walker, Julie Scharper and Liz Bowie contributed to this article.