In the Philadelphia suburbs, more than four out of five schools in the suburbs met the mark.
Overall, 46 percent of 259 city schools met state standards. That's down from 59 percent in 2010.
Among charters, 46 of 73 met state standards.
In the suburbs, 81 percent of 497 schools made Adequate Yearly Progress compared to 88 percent last year.
Statewide, the percentage of schools meeting the standard was 75.1 percent. That's down from 82.6 percent in 2010.
Ron Tomalis, Pennsylvania's state education secretary, said in an interview that he's happy to see the student gains which were about one percent. "To see the scores go up is always good - something to celebrate," he said.
Tomalis added, however, that only 39 percent of schools statewide met the Adequate Yearly Progress mark based on the test scores of all student groups. "That is a caution sign," he said.
Under the federal No Child Left Behind law, a school must show that all groups of its students, including special education, minorities and economically disadvanted, meet the standards. Students are tested in math and reading in grades three through eight and in 11th grade.
Though fewer schools met the mark this year, overall student performance on the PSSA improved statewide, with 77.1 percent of students scoring at or above grade level in math and 73.5 percent of student meeting or exceeding the mark in reading.
Individual student achievement in the Philadelphia district is also up, for the ninth straight year. Math scores rose 3 percentage points over last year, to 59 percent passing, and reading scores were up 2 points, to 52 percent passing.
The same information about student performance in the Philadelphia suburbs could not immediately be obtained.
Low-performing Philadelphia schools that were overhauled in the 2010-11 school year showed gains, too. Both Promise Academies - district-run schools with largely new staffs and longer days and years - and schools turned over to outside organizations as Renaissance charters improved their performance.
Tomalis also pointed out that the generally high percentage overall of students scoring at grade level does not hold true for all grades or all groups of students tested. In math, for example, 83.5 percent of third graders scored at or above grade level, but only 60.4 percent of 11th graders met the mark.
Several high-achieving area high schools, though performing much better than the state average, saw declines in 11th grade scores. Radnor High's reading score went down by about four percentage points and Lower Merion High School's reading numbers decreased by more than three percentage points.
Delaware County's Chichester Senior High improved its reading score by about 19 percentage points, though it still did not make Adequate Yearly Progress because one group--African American students--did not score high enough in math.
Statewide, only 37.9 percent of special education students performed at or above grade level in reading and only 52.2 percent of African American students scored at or above the grade level benchmark.
Many schools were tagged as failing because special education students did not score high enough.
In Delaware County's high-achieving Haverford Township School District, for example, the Chestnutwold Elemertary school failed to meet the state standard for special education students' reading scores, even though more than 83 percent of students overall are performing at or above grade level.
"To say that a school is not performing properly because a few kids who are by definition not learning at the same level as their peers don't make it up to an arbitrary standard - that's nuts," said board member Lawrence Feinberg. "This is a good school."
As for the special education students, he said, "our focus is on helping these kids learn as much as they can - and we do that."
While some school leaders were complaining, others were celebrating. Boys' Latin of Philadelphia Charter School, for example, was among the city's most improved performers in both reading and math. CEO David Hardy said he is proud, but not surprised. The school opened in 2007 and 2011 was only the second year of testing.
The school used benchmark tests and online math and reading programs to target students' areas of weakness, Hardy said. They made the PSSA test a competition, and students rose to the challenge, he added.
Hardy, expects the trajectory to continue. "In two years, we're really going to tear this thing up," he said. "We really know how to do it."
By 2014, 100 percent of all students and schools are supposed to be performing at grade level under the provisions of the No Child Left Behind law.
Last week, the Obama administration, saying that 100 percent student proficiency by 2014 is an unmeetable goal, announced that states could apply for a waiver of that requirement and adopt different targets, if they also agree to adopt a new approach for turning around the bottom 15 percent of schools.
Tomalis, a defender of No Child Left Behind, said Thursday that he has not decided whether the state will apply for the waiver.
He said that many states, including Pennsylvania, set standards for schools making Adequate Yearly Progress that called for little improvement in the early years and very steep gains in the last few years before 2014.
The prospect of achieving those gains over the next three years, he said, is "unrealistic." But the state, he said, does not necessarily want to replace the goals of the current No Child Left Behind Law with a new set of mandates that are included in the Obama administration waivers, so it is still looking at all options.
Contact staff writer Dan Hardy at 215-854-2612, email@example.com, or on Twitter @DanInq.